Fusarium oxysporum species complex (FOSC) includes important soilborne pathogens of various crops worldwide including formae speciales and physiological races that are reported to have unique associations with their specific hosts. In Victoria, F. oxysporum has been identified as the cause of collar and root rot, stunting and poor growth in processing tomatoes, resulting in significant yield losses to the industry however, little is known about its race composition. Such information is critical to the industry to inform cultivar selection. A collection of isolates from infected root and crown tissue of processing tomatoes in New South Wale, Victoria and Queensland Plant Pathology Herbarium were confirmed to be F. oxsyporum through multi-gene phylogenetic analyses based on four genomic loci: translation elongation factor-α (tef1-α), calmodulin (cmdA), tubulin (tub2) and the second largest subunit of nuclear RNA polymerase II (rpb2). Race composition of the pathogen population determined from sequence analyses of seven pathogenicity-related genes (uni, sp13, sp23, sprl, pg1, pg5 and pgx4), and twelve secreted in xylem (SIX) genes did not correlate with the isolates’ phylogenetic clustering. Most of the isolates formed the same clade with F. oxsyporum f. sp. lycopersici (FOL) race 3 and a few that did not clade with any known races of FOL. A subset of isolates used in a pathogenicity bioassay were able to cause significant growth reduction on processing tomatoes, regardless of their races. Incongruence of phylogenetic signal among housekeeping and pathogenicity-related genes, horizontal gene transfer and genetic recombination within FOSC is well established. Our research highlights the importance of complementing molecular markers with pathogenicity assays to characterise races in FOSC. Knowledge of the FOL races causing the disease will improve integrated disease management.