Phyloviewer is a web-based program for building phylogenetic trees based on multiple statistical inferences with the best fit model of sequence substitution. It also used in testing hypothesis on evolution process and testing the alternative topology of the phylogeny. Genome sequences of many eukaryotic species are publically available since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996. Especially, fungal and Oomycete sequencing projects are important due to severe pathogenic characteristics, providing comparative genomics environment of many potential and hypothetical pathogenecity related proteins. These protein sequences also have been utilized to answer many evolutionary questions: e.g. speciation of fungal kingdom with duplication process of gene families and patterns of horizontal gene transfer among various species. Phyloviewer has been utilized in many fungal databases as component, and provided very useful tool for archiving phylogeny and testing several evolutionary hypothesis. Here, we introduced the Phyloviewer, web-based integrated environment for phylogenomics study with fungi and Oomycete genome resources.