Forty-nine strains of the Fusarium oxysporum complex were isolated from five different sample locations within two neighboring pea fields. Of these, 39 strains were isolated from soil and 10 from pea plants showing symptoms of root rot. Twenty-eight of the isolates were tested for pathogenicity towards pea. Based on percentage discoloration of the roots and stem base, the isolates were divided into three groups: seven strains were pathogenic, 14 strains were weakly pathogenic, and seven strains were non-pathogenic towards pea. To assess the genetic relatedness of all 49 strains, gene genealogies were constructed from aligned DNA sequences from part of the translation elongation factor, nitrate reductase, beta tubulin, and mitochondrial small subunit rDNA. Maximum parsimony analysis of the combined data set yielded a single most-parsimonious tree containing three strongly supported clades which may represent cryptic species. No correlation was observed between the multigene phylogeny and pathogenicity toward pea, strain geographic origin and substrate (soil or plant) from which the strains were isolated. Strains that were non-pathogenic, weakly pathogenic or pathogenic sometimes shared the same multilocus genotype. These results suggest that strains pathogenic and putatively non-pathogenic to pea are very closely related genetically.