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Hypothesized most recent common ancestor of the patrilineal Jewish priestly caste known as Kohanim

Y chromosomal Aaron is the name given to the hypothesized most recent common ancestor of the patrilineal Jewish priestly caste known as Kohanim (singular "Kohen", also spelled "Cohen"). According to the traditional understanding of the Hebrew Bible, this ancestor was Aaron, the brother of Moses. While some early genetic studies were seen as possibly supporting the traditional biblical narrative, this view was subsequently challenged with some researchers arguing that the genetic evidence "refutes the idea of a single founder for Jewish Cohanim who lived in Biblical times." However, recent studies have provided further support for the model of descent from a common ancestor who lived in the First Temple period by demonstrating that Kohanim from different Jewish communities form a "tight cluster" which is "specific to the Jewish Cohens". The original scientific research was based on the hypothesis that a majority of present day Jewish Kohanim share a pattern of values for six Y STR markers, which researchers named the extended Cohen Modal Haplotype (CMH). Subsequent research using twelve Y STR markers indicated that nearly half of contemporary Jewish Kohanim shared Y chromosomal J1 M267 (specifically haplogroup J P58, also called J1c3), while other Kohanim share a different ancestry, such as haplogroup J2a (J M410).

The Kohen hypothesis was first tested through DNA analysis in 1997 by Prof. Karl Skorecki and collaborators from Haifa, Israel. In their study, "Y chromosomes of Jewish priests," published in the journal Nature, they found that the Kohanim appeared to share a different probability distribution compared to the rest of the Jewish population for the two Y chromosome markers they tested (YAP and DYS19). They also found that the probabilities appeared to be shared by both Sephardic and Ashkenazi Kohens, pointing to a common Kohen population origin before the Jewish diaspora at the destruction of the Second Temple. However, this study also indicated that only 48% of Ashkenazi Kohens and 58% of Sephardic Kohens have the J1 Cohen Modal Haplotype. Such genetic markers were also found in approximately 5% of Jews who did not believe themselves to be kohanim. ); CMH.1 means "within one marker of the CMH 6"; and CMH is the proportion with a 6/6 match. The final two columns show the conditional proportions for CMH.1 and CMH, given membership of Haplogroup J. The data show that the Kohanim were more than twice as likely to belong to Haplogroup J than the average non Cohen Jew. Of those who did belong to Haplogroup J, the Kohanim were more than twice as likely to have an STR pattern close to the CMH 6, suggesting a much more recent common ancestry for most of them compared to an average non Kohen Jew of Haplogroup J.

Thomas, et al. dated the origin of the shared DNA to approximately 3,000 years ago (with variance arising from different generation lengths). The techniques used to find Y chromosomal Aaron were first popularized in relation to the search for the patrilineal ancestor of all contemporary living humans, Y chromosomal Adam. Subsequent calculations under the coalescent model for J1 haplotypes bearing the Cohanim motif gave time estimates that place the origin of this genealogy around 6,200 years ago (95% CI: 4.5–8.6 Kybp), earlier than previously thought, and well before the origin of Judaism (David Kingdom, ~2.9 Kybp). The latest studies on the other hand have proposed coalescence estimates ranging between ~3,200 and ~2,570 years before present, which are in broad agreement with a progenitor who lived during the First Temple period. Following the discovery of the very high prevalence of 6/6 CMH matches amongst Kohanim, other researchers and analysts were quick to look for it. Some groups have taken the presence of this haplotype as indicating possible Jewish ancestry, although the chromosome is not exclusive to Jews. It is widely found among other Semitic peoples of the Middle East. Later research has been unable to confirm this (due to the fact that CMH was widely found among other Semitic peoples of the Middle East) although it has shown that some male Lemba have Middle Eastern ancestry. A historical critical reading of the biblical text suggests that the origin of the priesthood could have been much more complex, and that for much if not all of the First Temple period, kohen may have not (necessarily) synonymous with "Aaronide". Rather, this traditional identity seems to have been adopted sometime around the second temple period.

One source of early confusion was the low resolution of the available tests. The Cohen Modal Haplotype (CMH), while frequent amongst Kohanim, also appeared in the general populations of haplogroups J1 and J2 with no particular link to the Kohen ancestry. These haplogroups occur widely throughout the Middle East and beyond. On the other hand, Jewish populations were found to have a "markedly higher" proportion of full 6/6 matches, according to the same (2005) meta analysis. The detailed data confirm that the main cluster of haplogroup J1 haplotypes from the Yemeni appears to be some genetic distance from the CMH 12 pattern typical of eastern European Ashkenazi Kohanim, but not of Sephardic Kohanim.

While there is evidence from Josephus and rabbinic sources that this tradition existed [I. E. was practiced and believed] by the end of the Second Temple (1st century CE, nearly a millennium and a half after the tradition places Aaron), there is no further evidence to support its historicity. According to modern biblical scholarship, a historical critical reading of the biblical text suggests that the origin of the priesthood is much more complex, and that for much if not all of the First Temple period, kohen was not (necessarily) synonymous with "Aaronide". Rather, this traditional identity seems to have been adopted sometime around the second temple period. The authors state, in their "Abstract" to the article:
"These results support the hypothesis of a common origin of the CMH in the Near East well before the dispersion of the Jewish people into separate communities, and indicate that the majority of contemporary Jewish priests descend from a limited number of paternal lineages." However, the study did not support a single Y chromosomal Aaron from the biblical period, rather it showed a "limited number of paternal lineages" from around that period.

Behar's 2003 data Additionally, the haplotype that was commonly found in Ashkenazi Levites is of a relatively recent origin from a single common ancestor estimated to have lived around 1.5–2.5 thousand years ago. it was found that they do not share a common male ancestor within the time frame of the Biblical narrative. further speculating that the ancestor(s) were unlikely to have descended from Levites of the Near East. However, a Rootsi, Behar, et al. study published online in Nature Communications in December 2013 disputed the previous conclusion. Based on its research into 16 whole R1 sequences, the team determined that a set of 19 unique nucleotide substitutions defines the Ashkenazi R1a lineage. One of these is not found among Eastern Europeans, but the marker was present "in all sampled R1a Ashkenazi Levites, as well as in 33.8% of other R1a Ashkenazi Jewish males, and 5.9% of 303 R1a Near Eastern males, where it shows considerably higher diversity."

The Samaritan community in the Middle East survives as a distinct religious and cultural sect. It constitutes the oldest and smallest ethnic minorities in the Middle East, numbering slightly more than 800 members. According to Samaritan accounts, Samaritan Kohanim are descended from Levi, the Tsedaka clan is descended from Manasseh, while the Dinfi clan and the Marhiv clan are descended from Ephraim. Samaritans claim that the southern tribes of the House of Judah left the original worship as set forth by Joshua, and the schism took place in the twelfth century BCE at the time of Eli. The Samaritans have maintained their religion and history to this day, and claim to be the remnant of the House of Israel, specifically of the tribes of Ephraim and Manasseh with priests of the line of Aaron/Levi. Since the Samaritans have maintained extensive and detailed genealogical records for the past 13–15 generations (approximately 400 years) and further back, researchers have constructed accurate pedigrees and specific maternal and paternal lineages. A 2004 Y Chromosome study concluded that the lay Samaritans belong to haplogroups J1 and J2, while the Samaritan Kohanim belong to haplogroup E M35.