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Publications that describe the composition of the human Y-DNA haplogroup in different ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus, a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. We genotyped 224 men that identified themselves as ethnic Georgian for 23 Y-chromosome short tandem-repeat markers and assigned them to their geographic places of origin. The genotyped data were supplemented with the published data on haplogroup composition and location of the other ethnic groups of the Caucasus. We used multivariate statistical methods to see if linguistics, climate, and landscape accounted for geographical differences in frequencies of the Y-DNA haplogroups G2, J2, R1b, J1, and R1a. The analysis showed significant associations of (1) haplogroup G2 with well-forested mountains, (2) haplogroup J2 with warm areas or poorly forested mountains, and (3) haplogroup J1 with poorly forested mountains. R1b showed no association with environment. Haplogroups J1 and R1a significantly associated with Daghestanian and Kypchak speakers, respectively, but the other haplogroups showed no such simple associations with languages. Climate and landscape in the context of competition over productive areas among different paternal lineages, arriving in the Caucasus in different times, have played an important role in shaping the present-day spatial distribution of patrilineages in the Caucasus. This spatial pattern had formed before linguistic subdivisions were finally shaped, probably in Neolithic to Bronze Age. Later historical turmoil had little influence on the patrilineage composition and spatial distribution. Based on our results, the plausible scenario of postglacial expansions of humans and their languages to the Caucasus from the Middle East, western Eurasia, and the East European Plain is discussed.