The population and community dynamics of four monogeneans, Pseudodactylogyrus anguillae, P. bini, P. microrchis, and an unidentified Pseudodactylogyrus sp., on the gills of cultured Japanese eels, Anguilla japonica L., were investigated at two fish farms at Chaozhou, Guangdong Province, China. A total of 8,377 individual parasites were collected from sampling pond I (with more frequent chemical treatments for parasitic diseases: generally twice per month), including 338 P. anguillae, 7,388 P. bini, 491 P. microrchis and 160 Pseudodactylogyrus sp. At sampling pond II (with fewer chemical treatments for parasitic diseases: generally once during summer and winter months), 20,776 parasites were recovered, comprising 1,904 P. anguillae, 13,999 P. bini, 3,135 P. microrchis and 1,738 Pseudodactylogyrus sp. Monthly parasite community and population parameters, such as prevalence, mean abundance and species richness, varied irregularly and were not significantly correlated with water temperature at both fish farms. The infection parameters, however, exhibited a significant relationship with water temperature under indoor conditions. The diversity of monogenean communities in sampling pond II was higher than that in sampling pond I. These results may imply that the effects of water temperature exerted on the parasite population and communities were masked by human interference (drug implementation) in the fish ponds.