Genetically Indian Story of Indian Muslims

“I belong to two circles of equal size which are not concentric, one is India and the other is the Muslim World.” – Muhammad Ali Jauhar

It is a well-known fact that Islam came to North India through Muslims who came here at different times. Some of the Muslims came as invaders, others as traders, preachers or settlers. What is not known is how many Muslims can be traced back to their foreign lineage and how many are descendent of Indians who converted to Islam.

Historians and commentators discount the idea that majority of Muslims of India are of foreign origin. There is nothing in history that provides evidence for mass migration of Muslims to India. This logically leads one to conclude that a large number of Indians converted to Islam during sometime in the past.

It is interesting that a large number of North Indian Muslims have always claimed their ancestry to be of foreign origin. On the other hand, Sangh Parivar claimed that most Indian Muslims have Indian ancestry and they were forced to convert to Islam. Genetics is the study of heredity which can provide some clues to the origin of Indian Muslims.


All living beings are made of countless cells. Each cell has a central region called nucleus. This nucleus contains chromosomes that are inherited from parents. Humans have 23 pairs of chromosome. Father and mother contribute one chromosome for each pair; these chromosomes of a pair are identical in shape. Chromosomes are nothing but a long strand of chemical called DNA or deoxyribose nucleic acid. Sequence of chemical base on DNA encodes genetic information. Sequences of DNA that encodes for some specific function or characteristics are called genes.

Genetic information determines whether you will inherit your mother’s eyes or father’s baldness. Twenty-two chromosomal pairs are common between males and females. Twenty-third chromosomal pair, also known as sex-determining chromosome, is what gives unique characteristics to human males and females. In case of females two chromosomes of the 23rd pair are identical and are labelled XX. One X is from the father and the other from the mother. For males, 23rd chromosomal pair is labelled XY, X is contributed from the mother and Y comes from the father.

Y chromosome has genes that give a man male characteristics e.g. facial hair, baldness, etc. By comparing the Y chromosome’s DNA sequence, it is possible to say with some certainty if two males are related to each other or not. During the formation of human embryo, chromosomes from mother and father exchange bits of genetic codes in a process known as crossing over. Crossing over event is what makes every individual and their genetic code unique. Still much of the genetic code remains unchanged from generation to generation and therefore genetics is a way to determine ancestry.

However, nucleus is not the only place that has genetic material. Mitochondrion, which is an organ within the cell, powers the cell by generating energy. Mitochondria also contain a piece of DNA and this is found to be very useful in determining maternal ancestry. This DNA does not undergo the process of crossing over and these are passed from mother to sons and daughters in its entirety. By looking at the sequence of mitochondrial DNA we can conclusively determine the maternal ancestry of individuals.

In the field of genetics there are sequences of DNA called genetic markers. The frequencies of presence of genetic markers are used to make an estimate of how close two groups of people are to each other. If two groups have a particular genetic marker in frequency very close to each other, it is possible that they have come from a common ancestor. Presence or absence of many of these genetic markers can further provide evidence of that conclusion.


In 2001, a scientific paper published in Journal of Biosciences by Partha Majumdar of Indian Statistical Institute looked at the presence of these genetic markers also called haplotypes or haplogroups to study the ancestry of various social groups in India. He found that one haplotype in mitochondrial DNA (mtDNA) was present in all the groups that he looked at. Since it is present in high frequencies in almost all groups, it has to be the most ancient haplotype in Indian population. “The three populations in which this haplotype is not the most frequent are all inhabitants of Uttar Pradesh in northern India – Brahmins, Rajputs and Muslims,” Majumdar reported. This particular study involved upper and lower castes from North and South India as well as tribals.

This means that Brahmins, Rajputs and Muslims share a common maternal lineage. This is also the conclusion of a recent study by Terreros et al to be published in American Journal of Physical Anthropology. This study was jointly done by American, Spanish and Sanjay Gandhi Postgraduate Institute of Medical Sciences of India. They divided the Muslim group into Shia and Sunni groups and compared their mtDNA with other Indian social groups in North and South. Researchers were of the opinion that “… at the mtDNA haplogroup level, both of these Indo-Sunni and Indo-Shia populations are more similar to each other and other Indian groups than to those from the other regions.” It is remarkable that not only they found them similar to other Indian groups but that there was complete absence of any genetic marker found in West Asia.

The study looked at the genetic composition of mitochondrial DNA (mtDNA) of Sunnis and Shias of UP. Blood samples from 60 Sunnis and 59 Shias volunteers were taken for this study. Their mtDNA was analysed for specific genetic markers. Frequencies of the presence of these markers were compared to various groups in India and other countries.

While there are some differences among Sunnis and Shias in terms of their mtDNA, in general they were found to be closer to the larger Indian population.

Principal component analysis (PCA), a statistical tool that separates individuals on the basis of differences in their properties was employed to place each social group on a plot. According to this plot Shias and Sunnis are much closer to Brahmins, Bhargavas, and tribals from Karnataka than people from UAE, Yemen, Egypt, Iran, Iraq, and/or Central Asian countries. PCA generated a plot that showed three clear clusters – Souther Arabian Peninsula, North East African population in upper left quadrant, East Central Asian and Middle Eastern group in the lower right hand corner, and all Indian groups can be found closer to each other to the right.

The study conclusively proves that Indian Muslims are part of the genetic landscape of India. According to the paper “our results demonstrate that the mtDNA haplogroup M is present in the Indo-Shia and the Indo-Sunni Muslims at a frequency of 50-60%, which is similar to that found in Indian caste groups examined in this study and others.” M haplogroup is one of the genetic marker used in this study.

Further proof that Sunnis and Shias are far removed from other West Asian population is the fact that they lack haplogroups H, I, J, K, and T found among the Arab groups.


Not considering the theological and historical differences among Shias and Sunnis, there are some genetic differences between the two Islamic groups in India. M haplogroup is considered one of the ancient halogroups in India because it is found in high frequency among all Indian groups. Sunnis have M haplogroup frequency of 0.500 while Shias have it in 0.328 indicating that comparatively Shias are younger than Sunnis in Indian landscape.
Historically, we know that Shias arrived in India later than Sunnis; therefore, it is not surprising that frequency of M haplogroup is little lower in them. In light of this, it is really surprising that there are M sub-haplogroups that are present only in Shias and not Sunnis. Presence of these sub-haplogroups will also place Shia as part of the Indian genetic makeup.

Time to the most recent common ancestor or TMRCA analysis is a measure of how many generations two DNA are from a common ancestor, based on the number of mutations the two sequences differ in. According to this analysis, Sunnis and Shias are close to other Indian subgroups; though it suggests that Shias are younger than Sunnis to arrive in India.

The TMRCA and lower frequency of M haplogroup for Shias may be an indication of their late arrival in India but it could also mean that they had lesser marital interaction with other Indian population. However presence of M sub-haplogroups among Shias points to their strong Indian genetic connection. The best we can draw from these two conflicting evidence is that Shias are rooted in India but they had lesser admixture than Sunnis with other Indian groups.

R haplogroup which is common in high level among Indians is found in very low levels in Arab countries and almost none in African countries. Both Shias and Sunnis of India show high levels of R haplogroup just like other Indian groups.


We have seen enough evidence to say with confidence that mothers of Indian Muslims are genetically Indian. Historians are of the opinion that Muslim males who came to India usually married local females and settled down. Therefore, it is not surprising that mtDNA shows Indian Muslims having Indian genetic heritage.

As mentioned before, Y chrosome, which is passed from father to son, can be used to determine the genetic origin of Indian Muslim males. For Y chromosomes, there are may well known and well researched genetic markers that are used in genetic studies.

In an international study by Rosser et al in 2002, haplogroup E which is present in significant frequency in the Middle East and West Asia was not seen in any of the North Indian groups, including any of the Indian Muslim population. If most of the Muslims of India are of foreign origin then they should be genetically close to the population of Muslim region viz. West Asia or Central Asia.

Comparison of Y chromosomes of Indian Muslims with other Indian groups was published in 2005 in journal Current Science by Suraksha Agarwal of Sanjay Gandhi Postgraduate Institute of Medical Sciences. In this study 124 Sunnis and 154 Shias of Uttar Pradesh were randomly selected for their genetic evaluation. Other than Muslims, Hindu higher and middle caste group members were also selected for the genetic analysis.

Out of 1021 samples in this study, only 17 samples showed E haplogroup and all of them were Shias. The 11.30 frequency does place Shias closer to Iraqis, Turks and Palestinians.

Rossen et al reported several genetic markers of Y chromosomes and their frequencies in many population groups. HG-3 was found to be most frequent in Northern India. Among the groups in this study (Brahmins, Chamar, Muslim, and Rajput), Muslims have the highest frequency of 57.9%, next to them are Chamars with 44.4%. Rajputs and Brahmins also show high frequencies at 37.1 and 35.3 respectively. This haplogroup is present in very low frequencies among the West Asian populations.

HG-21 which is same as haplogroup E mentioned before was not found in any of the Indian population by Rossen. HG-1 is present in all Indian groups about the same level. HG-2 is present in high frequency among Brahmin, Chamar, and Rajput groups but missing from Muslims. Interestingly, HG-9 is present among Brahmins, Muslims and Rajputs but absent in Chamars. HG-26 haplogroups have a significant presence (15.8%) among Muslims and a low level (2.9%) among Rajputs but missing from Brahmins and Chamars. On the other hand HG-28 is present in Brahmins and Rajputs at almost identical level but missing entirely from Chamars and Muslims.

To conclude, study by Rossen et al looked at the 7 genetic markers. They found that all four Indian population groups were similar in 3 of these markers; in 2 markers Muslims were different from other groups. In one each, Muslims either were similar to Chamars or Brahmins and Rajputs.


Looking at the maternal and paternal genetic evidence, it is safe to assume that Indian Muslims are very much sons of the soil or as much as any other social group in India. It will not be surprising to find some evidence of foreign lineage among Muslims but in fact we find them at very low levels which suggest that a majority of Muslims are Indians who became Muslim or there was enough marital interaction with other Indian groups over the years.
If Indians were forced to convert then we would have seen Indian Muslims genetically closer to lower castes that are in probability are less likely to resist or more to gain socially by accepting an egalitarian faith. Contrary to this, we find evidence that brings Muslims closer to Brahmins and Rajputs for both maternal and paternal genetic markers.
In case of paternal genetic markers we find all Indians are similar. When they differ Muslims in half the cases are unique and in other half they are either in the same camp as higher castes or lower castes of Hindus.

All these studies had a smaller sample size and therefore a larger sample size can give us a better picture about the origin of Indian population in general and Indian Muslims in particular. But looking at all these studies even with a smaller sample size gives us a clear picture that does not contradict what historians have claimed. Islam came to North India through invaders, preachers and traders but an overwhelming number of Indian Muslims converted on their own accord and conversion was cutting across caste and social lines.

In the end, the quote from Muhammad Ali Jauhar sums up the mentality of Indian Muslims. We are proud of our heritage that we acquire from India and the other that we claim by being Muslims. Genetics or no genetics, this is what makes Indian Muslims a unique group.