Two types are known in the Kanzawa spider mite, Tetranychus kanzawai (K and T; see Gotoh et al., 1999), which differ in host range and have a unidirectional incompatibility. Prior to DNA analyzes, crossing between females of a known K type and males of each of 17 strains collected in Japan showed that six of the strains were of the K type, five were the T type and the rest consisted of a mixture of the two types. In order to elucidate the genetic diversity and phylogenetic relationship of T. kanzawai in Japan, we analyzed the DNA sequences of two regions - the internal transcribed spacer 1 (ITS1) of the nuclear ribosomal DNA (rDNA) and a fragment of the cytochrome oxidase subunit I gene (COI) of mitochondrial DNA - using 11 strains (six K-type strains and five T-type strains). Base substitutions were detected on 25 sites of COI (375 bp) and 19 sites of ITS1 (486 bp), resulting in eight and 17 haplotypes, respectively. The phylogenetic trees constructed using the DNA sequences failed to clearly distinguish between the two types. The results suggested that the T type was derived from the K type.