Several isolates were collected from apple, pepper, strawberry, cucumber and tomato having typical gray mold symptoms. All the isolates were identified as Botrytis cinerea by using morphological characteristics and PCR-RFLP method. It was difficult to analyze the phylogenetic relationship of these isolates by using ITS region, HSP60 and G3PDH because these genes were highly homologous in their nucleotide in inter-species of B. cinerea and intra-species of genus Botrytis. However, phylogenetic analysis using combined sequences (RPB2, HSP60 and G3PDH genes) clearly showed that all isolate of B. cinerea were different from Botrytis spp. Furthermore, it was also confirmed that strawberry isolate was distantly related to apple, pepper, cucumber and tomato isolates that were closely related to each other in nucleotide level.