Since 2012, a severe postharvest rot of mango fruits (cv. Lippens) has been found in Okinawa Prefecture, Japan. A fungus frequently isolated from the diseased fruits was identified as Neofusicoccum parvum based on morphological, cultural characteristics and sequence similarity of rDNA-ITS region and EF1-α gene. The isolates reproduced the symptoms on mango fruits after inoculation and were reisolated from the inoculated fruits. Neofusicoccum parvum is proposed as another pathogen of stem-end rot of mango in Japan.