Abstract:In order to screen out a molecular methods that is suitable for quarantine purpose and can be used in fast identifying the three brown rot pathogens, Monilinia fructicola, Monilinia laxa and Monilinia fructigena, the method developed by Lane et al. based on the morphological characteristic was firstly used to identify 58 isolates of Monilinia from stone and pome fruits collected from Beijing, Shandong, Hebei, etc. in China. Among the 58 isolates, 53 were identified as M.fructicola, two were M.laxa and the other three were M.fructigena. Then, three molecular identification methods that have been developed previously were compared using these isolates and the standard isolates of these three species. With the method developed by Ioos et al., species-specific bands of respective species were amplified from the standard isolates of three respective species, 53 isolates identified as M.fructicola and two isolates identified as M.laxa, but species-specific bands of two different species were amplified from two of three isolates iden- tified as M.fructigena. With method developed by Ma et al., species-specific bands of respective species were amplified from the standard isolate and 53 isolates of M.fructicola and the standard isolate of M.laxa. But bands that supposed to be specific to M.fructicola were also amplified from two isolates of M.laxa, and the band supposed to be specific for M.laxa were amplified from three M.fructigena isolates. No product had been obtained from the standard isolates of M.fructigena. With method of Cote et al., species-specific band was only yield from sixteen isolates of M.fructicola. No product had been obtained from other isolates including the standard isolates. These results showed that the method of Ioos et al. can be used in identification of M.fructicola and M.laxa, the method of Ma et al. can be used only in identification of M.fructicola. The molecular identification method for M.fructigena remains to be investigated.