The Pythium ultimum species complex is comprised of two morphological varieties: var. ultimum and var. sporangiiferum. Previous efforts to resolve whether the two varieties are genetically distinct have produced conflicting results. Using 29 isolates of Pythium ultimum - twelve isolates of var. sporangiiferum and seventeen isolates of var. ultimum, multi-gene genealogies were created from both newly identified highly variable genes and previously identified genes. Observed conflict between species estimates given by nuclear and mitochondrial gene regions resulted in two separate studies. The first examined multiple nuclear genes to resolve the species complex, while the second tested the suitability of mitochondrial genes for phylogenetic analysis. Nuclear multi-gene genealogies found that the Pythium ultimum species complex is comprised of four genetically distinct species, while mitochondrial multi-gene genealogies indicate that the mitochondrial genome of Pythium ultimum is single copy, non-recombinant and uniparentally inherited.