This list of sequenced fungi genomes contains all the fungal species known to have publicly available complete genome sequences that have been assembled, annotated and published; draft genomes are not included, nor are organelle only sequences.
Chytridiomycota includes fungi with spores that have flagella (zoospores) and are a sister group to more advanced land fungi that lack flagella. Several chytrid species are pathogens, but have not had their genomes sequenced yet.
Zygomycota is probably a polyphyletic group that contains basal fungal lineages.