In order to examine whether the viral population is affected by intramucosal transmission, we analyzed the viral genotypes first detected in peripheral blood mononuclear cells (PBMCs) after intravaginal inoculation, before virus antibodies were detectable, and compared them with those in the inoculum. Three female cynomolgus macaques were inoculated intravaginally and a fourth was inoculated intravenously with polyclonal simian immunodeficiency viruses (SIVmac32H). The provirus genomes which first appeared in PBMC were sequenced in the V1 to V2 region of the SIV envelope gene. A comparison of the sequences obtained from each monkey revealed a homogeneous or heterogeneous viral population depending on the infection route. In the intravenously inoculated monkey, the viral population was heterogenous and was similar to that in the virus inoculum. On the other hand, in the intravaginally inoculated monkeys, single genotypes (in two monkeys) and one genotype with a slight variation (in one monkey) were found, but they were different from each other, having no characteristic sequences in the V1 to V2 region in common. None of the genotypes found in the PBMC were major genotypes in the virus inoculum. These results suggest that some selective mechanism, which differs among individuals, restricts the viral population during mucosal transmission.