The isolate from a canine disseminated protothecosis was identified to be Prototheca wickerhamii by its morphological and biochemical characteristics. The isolate was grouped into a cluster identical to the type strain of P. wickerhamii, ATCC 16529(T) in phylogenetic trees based on the small subunit (SSU) and the 5' end of the large subunit (LSU) ribosomal DNA (rDNA); the cluster was close to that including the other Prototheca species. However, the strains of P. wickerhamii, SAG 263-11 and Pore 1283 belonged to a cluster different from the other isolates of Prototheca species and closely related to those of Auxenochorella species. Therefore, P. wickerhamii could be divided into two distinct genetic groups, one group close to the other Prototheca spp. including a standard strain of P. wickerhamii, and another group consisting of isolates previously reported to be close to the Auxenochorella species.