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This study aimed to identify fungal species associated with trunk diseases of sweet cherries (<i>Prunus avium</i>) in several commercial cherry orchards in Beijing, Guizhou and Shandong provinces, China. In total, eighteen fungal strains that fitted well into the species concept of <i>Diaporthe</i> were isolated. Based on both morphological and multi-locus phylogenetic analyses of internal transcribed spacer region (ITS), beta-tubulin (<i>tub-2</i>), calmodulin (<i>Cal</i>) and translation elongation factor 1-α (<i>tef1–α</i>) sequencing data, fourteen isolates were identified as <i>Diaporthe eres</i>, while four isolates were classified as <i>D. hongkongensis</i>. Here, we report <i>D. hongkongensis</i> causing sweet cherry branch dieback disease and, further, we confirmed the host association of <i>D. eres</i> with sweet cherries in China. A pathogenicity assay revealed the ability of both <i>D. eres</i> and <i>D. hongkongensis</i> to cause shoot necrosis and stem lesions on <i>Prunus avium</i> cv. ‘Brooks’ (mean lesion lengths of 1.86 cm and 1.56 cm, respectively). The optimal temperature for the growth of both <i>Diaporthe</i> species was tested. The optimal growth temperature for <i>D. hongkongensis</i> was 30 °C, and the 25–28 °C temperatures were the most favorable for the growth of <i>D. eres</i> strains. This research advances the understanding of fungal trunk diseases in fruit crops, particularly gummosis and branch dieback disease in Chinese cherry orchards, and will aid growers in making decisions about cultural practices and disease management.