Recently developed molecular techniques facilitate the re-evaluation of phylogenetic relationships and taxonomic classification. This study evaluates 11 Japanese Phytophthora strains that previously had been identified morphologically, and three additional strains that had remained unidentified. The eleven previously identified strains exhibited low sequence homology with the species they were assigned to originally, but high homology with P. hedraiandra, P. multivora, P. niederhauserii, P. sansomeana, P. sp. kelmania, and P. sojae. The three previously unidentified strains showed low homology with representative strains of P. nicotianae or P. palmivora, according to previous analysis based on rRNA gene internal transcribed spacer (rRNA gene ITS), rRNA gene large sub-unit (LSU) and cytochrome c sub-oxidase (cox)1 sequences. To confirm previous phylogenetic identifications, we sequenced more two genes, β-tubulin and translation elongation factor 1 alpha (EF1-α), performed phylogenetic analyses in different gene combinations and obtained results that were in line with morphological data. The re-identified species P. hedraiandra, P. multivora, P. niederhauserii, P. sansomeana, and P. sp. kelmania are new to Japan, adding to the Phytophthora biodiversity in this country. Taken together, this and previous phylogenetic studies indicate that cox1 is a dependable gene for Phytophthora identification.