Three strains 138#,233# and 366# were isolated from infected strawberry, blueberry and cherry fruit. All the fungal pathogens were identified as Botrytis Nees by morphological characterization and rDNA ITS analysis. The results obtained by the analysis of both morphological characterization and rDNA ITS sequence showed that strains 138# and 366# belonged to the same species and were closely related to B. cinerea (KJ937044.1). In contrast, strain 233# had a close phylogenetic relationship with B. elliptica (EU519207.1). The biolog microbial identification system with FF microplate was applied for 95 different carbon and nitrogen sources utilization tests of three pathogens, and the result of the carbon metabolic fingerprinting showed that three strains had 67 carbon sources in common, including fifty-six optimal carbon sources, one available carbon source and ten unavailable carbon sources. In addition, metabolic profiling revealed that three fungi were all closely related to B. cinerea Pers. BGA and 233# was the nearest to B. cinerea Pers. BGA.