Sapindus mukorossi Gaertn. (Sapindaceae), soapberry is an important biodiesel tree in southern China. In recent years, leaf spot disease on soapberry has been observed frequently in soapberry germplasm repository, Jianning County, Sanming City, Fujian Province, China. The symptoms initially appeared as irregular small yellow spots, and the center of the lesions became dark brown with time. Three fungal isolates from lesions were collected. Koch's postulates were performed, and their pathogenicity was confirmed. Morphologically, α conidia from diseased tissues were 1-celled, hyaline, smooth, clavate or ellipsoidal, biguttulate, and measured 6.2–7.2 × 2.3–2.7 μm. In addition, the three isolates in this study developed three types (α, β, and γ) of conidia on PDA, and their morphological characteristics matched those of Diaporthe. A phylogenetic analysis based on ITS, TEF, TUB, HIS, and CAL sequence data determined that the three isolates are a new species of Diaporthe. Based on both morphological and phylogenetic analyses, the causal fungus, Diaporthe sapindicola sp. nov. was described and illustrated.