This study used Restriction Fragment Length Polymorphism (RFLP) and Internal Transcribed Spacer (ITS) PCR sequencing technology to identify 60 isolates of suspected pathogenic Saprolegnia strains collected from 7 provinces including Shanghai, Jiangsu, Jiangxi, Sichuan, Hebei, Zhejiang and Hubei. Taxonomical analysis was also performed with strains of Saprolegnia reported in recent years. Comparative studies of physiological and molecular characteristics of pathogenic strains isolated from both infected fishes and eggs were carried out. The results showed that the 60 isolates could be classified into 10 special genetypes and all the isolates belonged to the clade of S. ferax, S. australis and S. parasitia by ITS-RFLP. Based on the phylogenetic tree, S. ferax and S. parasitia were the main Chinese pathogenic Saprolegnia strains. In addition, no significant difference existed in morphology of both asexual and sexual organs between the two S.ferax isolates from infected fishes and eggs. The same isolate could infect amphibian eggs and fishes. Thus, S.ferax and S.parasitia were identified as major pathogenic strains for both fish and eggs. The results could serve as a reference for the control of Saprolegniasis.