In July 2013, a severe postharvest rot of mango fruits (cv. Lippens), with symptoms identical to stem-end rot caused byLasiodiplodia theobromaeorNeofusicoccum parvum, was found in Okinawa Prefecture, Japan. From affected fruit,Diaporthespecies were consistently isolated. The isolates reproduced the original symptoms in healthy mango fruits after inoculation and were re-isolated from the inoculated fruits. Based on morphology and a phylogenetic analysis of rDNA-ITS,CAL,H3,EF1-alpha, andTUB, the isolates were classified into twoDiaporthespecies (Clade I and Clade II). In terms of susceptibility to procymidone, a registered fungicide against mango stem-end rot in Japan, the twoDiaporthespecies were less sensitive than previously reported mango stem-end rot pathogens and had MIC and EC(50)values higher than the standard concentration applied.