Strawberry crown rot is a serious fungal disease that poses a great threat to strawberry production in the growth cycle. The dominant pathogens of strawberry crown rot pathogens were different in different periods. The main pathogen of strawberry crown rot at the seedling stage is unclear. In this study, 74 Colletotrichum spp. were isolated from 100 strawberry plants at the seedling stage. Based on the morphological observations and phylogenetic analysis of multiple genes (ACT, CAL, CHS, GAPDH, and ITS), all 74 tested isolates were identified as C. gloeosporioides species complex, including 69 isolates of C. siamense and 5 isolates of C. fructicola. Colletotrichum siamense is the main pathogen of strawberry crown rot at the seedling stage in Zhejiang, China. The sterol demethylation inhibitors (DMIs) were used to control strawberry crown rot, and their target was the CYP51 gene. The role of the homologous CYP51 gene in growth, reproduction, pathogenicity, and sensitivity to DMI fungicides in C. siamense has not been determined. Our study found that the pathogenicity of CsCYP51A deletion mutants to strawberry leaves and stems was weakened. The hyphae growth rate of CsCYP51B deletion mutants was significantly slower than that of the wild type, but the sporulation and appressorium production rates increased. CsCYP51B deletion mutants had significantly increased pathogenicity to the stem. Deletion of CsCYP51A led to increased sensitivity to prothioconazole, ipconazole, hexaconazole, triadimefon, prochloraz, tebuconazole, metconazole, propiconazole, and difenoconazole. CsCYP51B deletion mutants were more insensitive. Our results indicate that the effect of the homologous CsCYP51 gene on hyphae growth, pathogenicity, and sensitivity to DMI fungicides differs.