Gray-mold neck rot is an important disease affecting onion (Allium cepa L.) production areas in Japan including Hokkaido, the northernmost region. We examined 10 representative isolates of Botrytis spp. collected from onion bulbs with symptoms of gray-mold neck rot in Hokkaido from 2009 to 2012. We analyzed conidial morphology and the number of nuclei in these isolates. Polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis was performed to identify the species. Five of the 10 isolates were identified as B. aclada; the remaining were identified as B. allii. From 2011 to 2017, we collected additional isolates from 50 fields in eight regions of Hokkaido and analyzed them with PCR–RFLP to clarify the distribution of Botrytis spp. Of the total 89 isolates, 63 were identified as B. allii and the remaining as B. aclada. B. allii was isolated from all eight regions of Hokkaido, whereas B. aclada was isolated from six regions, demonstrating the wide distribution of both species in Hokkaido and the tendency for B. allii to dominate. An inoculation test revealed the two species were pathogenic on onion bulbs. This report is the first of B. aclada causing onion gray-mold neck rot in Japan.