Chytrid is a common name to include all members of the phylum Chytridiomycota. They are present in both aquatic habitates and soils. Most aquatic forms are found in fresh water, there are some marine species that live mostly in estuaries. This is the first report about the diversity and ecology of chytrids in Taiwan. The first objective of this study was to survey the abundance and diversity of chytrids in freshwater wetlands. Twenty-nine isolates were identified as eight genera thirteen species of Chytridiales and Hyphochytriales. Rhizophydium is the dominant genus. Rhizophydium laterale is the ubiquitous and dominant species. The second objective was to periodically ecological survey of chytrids in reservoirs and river. Fifteen isolates were identified as three genera seven species in Tsengwen Reservoir and Mudan Reservoir. Ninteen isolates were identified as five genera nine species in Tsengwen river estuary and Gaoping river. The dominant species from individual collecting area is different. The similarity among these collecting sites are very low. Results reveal that diversity of chytrids in wetlands is higher than in river, the lowest is in reservoir. We applied principal component analysis (PCA) techniques to analyse water parameters which may influence the distribution of chytrids in the reservoir and river. Result reveal that physicochemical parameters are important determinants of the distribution of chytrids in their native environment.