Human T cell lymphotropic virus type II (HTLV-II) is a deltaretrovirus endemic in Indian populations living in Central and South America, among Pygmies tribes from Central Africa, and epidemic among injecting drug users (IDUs) in the United States, Europe, Southeast Asia, and South America. To date only the HTLV-IIa subtype has been demonstrated among Brazilians (Amazon basin Indians, blood donors, and IDUs). We analyzed HTLV-II isolates from 12 individuals living in the urban area of Porto Alegre, Southern Brazil, identified as seropositive for HTLVI/II in a blood donation. The HTLV-II long terminal repeat (LTR) region was sequenced and compared with nucleotide sequences of isolates HTLV-IIa (Mo), HTLV-IIb (NRA) prototypes. Phylogenetic analysis of the LTR region demonstrated that seven new isolates clustered together with American Indians HTLV-IIb isolates, and five new HTLV-IIa isolates clustered within the HTLV-IIa Brazilian subgroup, named the HTLV-IIc subtype. Both HTLV-IIa and IIb seem to be endemic in the urban area of Porto Alegre, South of Brazil, and could have reached this region via the Amazon basin and the Pacific Coast ancient human migratory pathways. To our knowledge this is the first study demonstrating the presence of HTLV-IIb among the urban population in Brazil.