Twelve Blastocystis isolates from primates were analyzed genetically by polymerase chain reaction (PCR) using diagnostic primers and PCR-restriction fragment length polymorphism (RFLP) of SSUrDNA. Two distinct genotypes, subtype 1 and a variant of subtype 1, were detected in two and six of the 12 isolates, respectively. The RFLP profiles of the isolates designated as subtype 1 were identical to the profile of ribodeme 1. The RFLP profiles of the six isolates designated as variants of subtype 1 were different from the profile of the variant of subtype 1 from a human reported previously. The other four isolates were not amplified with any diagnostic primers, but three of them showed the same RFLP profiles as ribodeme 6. This study was the first genomic analysis of Blastocystis isolates from primates, and showed the genetic similarity between the isolates from primates and the genotypes of Blastocystis hominis. However, it was unclear whether the isolates examined were zoonotic or not. Therefore, it is necessary to reveal the phylogenetic relationships between the isolates from primates and the multiple genotypes of B. hominis.