The aim of this paper is to develop an applicable Random Amplified Polymorphic DNAs (RAPD) method for genotyping strain, and discuss the possibility of using the RAPD method to trace strain transmission route. Four different pretreatment methods were used on the genomic DNA component, and the best adaptive extract method was selected for RAPD. Different RAPD primers sequence was used for amplification and their differentiating capabilities for strains were compared. Applicable RAPD primer was selected for genotyping and then applied into transmission detection. The results show that the so called cetyltrimethylammonium bromide (CTAB) method for extracting genomic DNA could give integrated genomic DNA and give out relatively better RAPD fingerprint maps, subsequently, using selected RAPD primer could give out a group of amplification polymerase chain reaction bands. The fingerprint maps from different strains were distinctive. Some main segments were common to all the strains tested. Some segments were different among the strains. According to the fingerprint maps and similarity index of different isolates, isolates from a pair of sex-partners were very similar. Based on these findings, the best extracting method and suitable RAPD primer were chosen. The RAPD fingerprint maps could type effectively and could be used as an additional approach in molecular epidemiology for tracing infection sources.