A previous analysis of mtDNA variation in the Caucasus found that Indo-European-speaking Armenians and Turkic-speaking Azerbaijanians were more closely related genetically to other Caucasus populations (who speak Caucasian languages) than to other Indo-European or Turkic groups, respectively. Armenian and Azerbaijanian therefore represent language replacements, possibly via elite dominance involving primarily male migrants, in which case genetic relationships of Armenians and Azerbaijanians based on the Y-chromosome should more closely reflect their linguistic relationships. We therefore analyzed 11 bi-allelic Y-chromosome markers in 389 males from eight populations, representing all major linguistic groups in the Caucasus. As with the mtDNA study, based on the Y-chromosome Armenians and Azerbaijanians are more closely-related genetically to their geographic neighbors in the Caucasus than to their linguistic neighbors elsewhere. However, whereas the mtDNA results show that Caucasian groups are more closely related genetically to European than to Near Eastern groups, by contrast the Y-chromosome shows a closer genetic relationship with the Near East than with Europe.