Phytophthora is a major genus of plant pathogens within the diploid, fungi-like Oomycota. A controversial issue in Phytophthora phylogeny and taxonomy involves P. cryptogea and P. drechsleri. In order to evaluate the phylogenetic lineages among isolates assumed to be P. cryptogea and P. drechsleri and their evolutionary relationship with related species, a worldwide collection isolates assigned to either P. cryptogea or P. drechsleri were assessed for morphological, physiological and molecular traits. Multiple gene genealogy analyses were performed on regions of nuclear and mitochondrial gene sequences. The present studies established the fact that P. drechsleri and P. cryptogea are distinct species. Data show that P. drechsleri is a homogenous species whereas P. cryptogea has considerable molecular variability and illustrates intraspecific variations. Species-specific primer sets were designed and evaluated for P. cryptogea and P. drechsleri identification based on ITS region of rDNA and mtDNA. The present work could be useful for specialist in mycology, plant pathology or molecular biology.