Chromosomal DNAs of 22 strains in 7 formae speciales (f. spp.) of Fusarium solani were compared by pulsed field gel electrophoresis (PFGE) and gene mapping on the chromosomes. Using PFGE, complete separation of the full components of the genome was not attained, due to the limited resolution of large chromosomes, but 5-12 chromosomes with sizes of 0.6-5.7 Mbp were resolvable for every strain. Although each strain had a unique banding profile, similarity in the banding profile was noticed among strains of the same (f. sp.). In gene mapping, the ribosomal RNA gene (rDNA) and putative pathogenesis-related genes encoding kievitone hydratase (khs), pisatin demethylase (pda) and pectate-degrading enzyme (pelA) were located on the chromosomes separated by PFGE. rDNA was always detected on the stacked large bands of 5.2-5.7 Mbp. The khs gene was detected on a chromosome of 2.8-5.4 Mbp in all f. sp. phaseoli strains and one strain of f. sp. pisi. The pda gene was detected on a chromosome of 1.4-5.6 Mbp in f. sp. pisi and pelA was localized on a chromosome of 2.3-2.9 Mbp in f. spp. pisi, xanthoxyli, batatas and mori. The results of PFGE and Southern blot hybridization supported the idea that each f. sp. of F. solani (or mating population of the teleomorph Nectria haematococca) has a distinctive genomic organization, as previously inferred from molecular phylogenetic analyses.