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Pestalotiopsis fungi are widely distributed all over the world, mainly as plant pathogens, endophytes or saprobes from multiple hosts. In this study, the sequence data analysis based on internal transcribed spacer (ITS), partial beta-tubulin (tub2) and partial regions of translation elongation factor 1 alpha (tef1α) combined with morphological characteristics was used to identify strains isolated from the diseased leaves of Aporosa dioica and Rhaphiolepis indica, as well as some rotted leaves from Yunnan and Hainan Provinces in China as three new species, viz., Pestalotiopsis aporosae-dioicae sp. nov., P. nannuoensis sp. nov. and P. rhaphiolepidis sp. nov.