Botrytis cinerea is the causal agent of gray mold disease on more than 220 plant species. B. cinerea is considered as one of the most important pathogens responsible for post harvest decay in the world. B. cinerea has a number of cryptic species that are morphologically similar with B. cinerea and live in sympatry with B. cinerea on plant hosts. In the present study, pomegranate fruit samples with gray mold symptoms were collected from cold storages in Iran to investigate the presence of B. cinerea cryptic species. After isolation and purification, single conidia from isolates plated on PDA in petri dishes and incubated at 25 ℃ under dark condition for two weeks. A total of 10 isolates from Botrytis genus were achieved. Genomic DNA was extracted. In order to identify cryptic species, an 1171 bp fragment of Bc-hch gene, a homolog of Nc-het-c (Related to vegetative incompatibility locus of Neurospora. crassa) gene was amplified with specific primers. By using Hhal restriction enzyme for enzymatic digestion of PCR product, six fragments were generated that showed two banding patterns among isolates. The pattern of five bands was the same among all isolates but the length of the largest fragment was 601 bp in one isolate (similar to the banding pattern of cryptic species) while in other isolates, the length of the largest fragment was 517 bp (similar to the banding pattern of B. cinerea) . To identify this species, three genes (HSP60, RPB2 and G3PDH) were partially amplified and sequenced. Blast analysis of three sequences showed 99% similarity with Botrytis sinoviticola. On PDA at 25 ℃ under dark condition for two weeks, B. sinoviticola formed whitish colony with abundant sclerotia but B. cinerea formed gray colony with a few sclerotia. Moreover, B. cinerea colony grew faster than the B. sinoviticola colony and no other distinctive morphological characteristics was found between these two species. This is the first report of B. sinoviticola on pomegranate fruit in the world and first report of presence of the fungus for mycobiota of iran.