Fusarium oxysporum (Fo) is a species complex that encompasses genetically and phenotypically diverse strains, some of which are major soilborne pathogens of economically important plants. Members of the Fo species complex (FOSC) are ubiquitous in soil and have been found in a wide range of ecosystems. In contrast to the broad collective host range of plant pathogens in the FOSC, individual pathogenic strains are typically host specific, only causing disease in one or a few related plant species. Genomics data and tools have begun to provide new insights into how pathogenicity may have evolved as well as the nature of virulence factors and their roles. The most notable discovery is that horizontal chromosome transfer within the species complex seems to a main mechanism underlying polyphyletic origins of pathogenicity to specific plants. We here summarize Fo genome structure and notable features in comparison with other fungi. In addition, we highlight key experimental tools that have made Fo an excellent "soilborne fungal disease" model. Rapidly increasing availability of genome sequences from many Fo strains presents unprecedented opportunities for systematic analysis of the evolution, ecology, and pathology of the FOSC.