To clarify the ethnic specificity of human T cell leukemia virus type I (HTLV-I) and type II (HTLV-II) carriers among Colombian native Indians, we investigated the geographic distribution of HTLV-I and HTLV-II seroprevalence among the isolated ethnic groups of Mongoloid origin in the Andes highlands and the Atlantic coast of Colombia. HTLV-I carriers were found in 1.6% (1/62 samples) of Inga, 8.5% (5/59) of Kamsa, and 0% (0/55) of Cumbal Indians who live in the Andes highlands at 3000 m above sea level. On the other hand, HTLV-II carriers were found in 4.1% (5/123) of Wayuu Indians, who live in the Guajira region of the Atlantic coast of Colombia at a distance of 1000 km from the Andes highlands. This ethnic specificity of HTLV-II was similarly observed among Guahibo Indians in the Orinoco. The seroprevalence of HTLV-I and HTLV-II was mutually exclusive among Inga, Kamsa, and Wayuu Indians. These results suggest that HTLV-I and HTLV-II may have evolved among Mongoloid populations and been independently transmitted among two different lineages of Colombian native Indians, Andes highlanders and Atlantic coast lowlanders.