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Unlike most pathogenic oomycetes, <i>Pythium insidiosum</i> infects humans and animals instead of plants. <i>P. insidiosum</i> has three clinically relevant genotypes/clades that cause a severe disease called pythiosis. To develop strategies for infection control, it is necessary to understand the biology and pathogenesis of this pathogen. Investigating the evolutionary mechanisms behind the host-specific adaptation is vital, and comparative genomic analysis can help with this. To facilitate genomic analysis, an online bioinformatics tool called <i>P. insidiosum</i> (Pins) Gene Table v2.0 was developed. This tool includes genomic data from 37 genetically diverse <i>P. insidiosum</i> strains and four related species. The database contains 732,686 genes, grouped into 80,061 unique clusters and further divided into core and variable categories at genus, species, and genotype levels. A high-resolution phylogenomic relationship among <i>P. insidiosum</i> strains and other oomycetes was projected through hierarchical clustering and core gene analyses. 3156 <i>P. insidiosum</i>-specific genes were shared among all genotypes and may be responsible for causing disease in humans and animals. After comparing these species-specific genes to the MvirDB database, 112 had significant matches with 66 known virulence proteins, some of which might be involved in vascular occlusion, which is a pathological feature of pythiosis. The correlation of genotypes, geographic origins, and affected hosts of <i>P. insidiosum</i> suggests that clade-I strains are more specific to animals, while clade-II/III strains are more specific to humans. The clade-specific genes might link to host preference. In summary, Pins Gene Table v2.0 is a comprehensive genome database accessible to users with minimal bioinformatics experience for the analysis of <i>P. insidiosum</i> genomes.