species are commonly isolated from environmental and clinical samples. As common causes of zoonotic mycosis, species may result in localized or disseminated infections, posing considerable threat to animal and human health. However, the pathogenic profiles of different species varied, in virulence, geographic location and host ranges, which have yet to be explored. Analysing the genomes of species are useful for understanding their pathogenicity. In this study, we analyzed the whole genome of 12 species and six isolates from different clinical samples in China. By combining comparative analyses with Kyoto Encyclopedia of Genes and Genomes (KEGG), Carbohydrate-Active enZymes (CAZy), antiSMASH, Pfam, and PHI annotations, species showed exuberant primary and secondary metabolism processes. The genome sizes of four main clinical species, i.e., , , , and were significantly smaller than other environmental and clinical species. The contracted genes included mostly CAZymes and peptidases genes that were usually associated with the decay of plants, as well as the genes that were associated with the loss of pathogenicity and the reduced virulence. Our results could, to some extent, explain a habitat shift of species from a saprobic life in plant materials to a pathogenic life in mammals and the increased pathogenicity during the evolution. Gene clusters of melanin and clavaric acid were identified in this study, which improved our understanding on their pathogenicity and possible antitumor effects. Moreover, our analyses revealed no significant genomic variations among different clinical isolates of from different regions in China.