Genomic fingerprints of 29 isolates of the pathogen Phytophthora parasitica from different hosts were analyzed by using 13 RAPD primers selected from 300 random primers with abundant polymorphisms. Genomic DNA from different isolates were amplified with the 13 selected primers and 139 marked bands were produced, of which 133 bands were polymorphic, accounting for 95.7% of the total bands produced. Based on the genetic distance, a dendrogram was constructed with the software PopGene Version 1.31, and the 29 tested isolates were divided into five genetic groups. Analysis showed that the genetic variation was very rich among the tested isolates. The isolates from Nicotana tabaccum (tobacco), N. glutinosa (tobacco),Chimonanthus praecox (wintersweet), Yucca spp. (beargrass) and Passiflora edulis (passionflower) were clustered into one group, and showed high relativity with their hosts. The similarity of Lycopersicum esculentum (tomato) isolates was about 60.9%, and they could be clustered into two distinct groups. The similarity of the five isolates from Sophora chinensis (sophora) was about 66.7%～88.4%, and they were also clustered into two groups when the dendrogram was constructed at the value point of 0.24 of the genetic distance. The results indicate that the host plants could have some effect on the genomic structure of the pathogen during the co-evolution between pathogen and their hosts.