Killer immunoglobulin-like receptors (KIR) exhibit extensive diversity and it has been observed that populations with different ethno-history, linguistic, geographic and genetic backgrounds can differ in KIR profile. In this context, we have investigated the KIR complex in three ethnic populations—Kachari (n = 108), Ahom (n = 104) and Adivasi (n = 101) of Assam, Northeast India. The three populations had 145 distinct KIR genotypes in 313 individuals typed. The two Mongoloid populations—Kachari and Ahom had close genetic affinities with their parental East Asian groups where the Kachari clustered with Chinese populations and the Ahom in another clade clustered with Thailand Bangkok and Polynesian populations. The Adivasi differed markedly from these Mongoloid populations in having higher KIR 2DL2, 2DS2, 2DS3 and 2DS5, but lower 2DL3 (P value <0.0001). Like the other native Indian populations, the Adivasi had higher share of Bx-haplogroup and C4Tx genotype (37/101). However, unlike other Indian populations, KIR 3DS1 gene frequency was lower in Adivasi (21%) and was comparable to the African populations. The neighbor-joining dendogram generated on the basis of KIR gene frequencies of our study populations with 43 world populations also placed the Adivasi with African populations. Interestingly, the three populations in the dendogram are consistent with their migration histories. In summary, our data suggest that KIR profile of the three ethnic populations displayed ethnic diversity and was consistent with their migration history thereby supporting the concept that KIR diversity may be used to understand genetic affinity and migration history of populations.