SummaryIran is a linguistically heterogeneous nation where Persian, Turkic and Arabic are the three main language families spoken. Based on their linguistic properties, Qashqais, Turkmens and Azeris are Turkic‐speaking people. The purpose of this study was to investigate whether any genetic relationship exists among the Turkic‐speaking Iranian subpopulations based on HLA class II gene diversity. HLA‐DRB1, DQA1 and DQB1 alleles were identified by PCR‐based methods in 100 Qashqais and 66 Turkmens, and the results were compared with our previously published HLA data for Azeris. Despite a number of allelic and haplotypic similarities, Qashqais, Turkmens and Azeris were not in the same clade of the phylogenetic tree. However, based on the results of principal coordinates analysis, they are grouped together with Kurds and Bakhtiaris. Contrary to their common linguistic features, the Turkic‐speaking people of Iran are closer to other Iranian subpopulations than to the people of Turkey and central Asia. Overall, it seems that linguistic criteria alone are not able to determine the relationships among these populations, and a combination of different kinds of anthropological information should be used to determine their actual phylogenetic relationships.