Background <p>The retrovirus Human T-lymphotropic virus type 1 is classified into different subtypes, and due to its low evolutionary rates, it can be used to explore geographic patterns of origin and dispersion of human populations. In Brazil, Transcontinental and Japanese subgroups, from the Cosmopolitan subtype, are the more common lineages, with prevalence rates notably higher among Japanese immigrants and their descendants. The study aimed to trace the history and circulation of the Japanese subgroup in Brazil using phylogenetic and populational analyses.</p> Methods <p>A total of 381 HTLV-1 long terminal repeat region sequences were retrieved from the GenBank database. Phylogenetic and molecular clock analysis were performed using Maximum Likelihood and Bayesian Inference methods. A median-joining network was constructed to assess the relationships among the haplotypes of the Japanese subgroup.</p> Results <p>This study found that the HTLV-1 LTR sequences from Japanese immigrants and their descendants in Brazil formed two major clades, Transcontinental (HTLV-1aTC) and Japanese (HTLV-1aJpn). Seventy-four haplotypes were identified in the haplotype network and the estimate of Japanese clade divergence dates 18,748&#xa0;years ago (95% CI13,348 to 24,767&#xa0;years).</p> Conclusion <p>Our study corroborates the recent migratory movements as the potential mechanism for HTLV-1aJpn introduction in Brazil.</p>