These results demonstrated the potential of the TaqMan real-time PCR targeting the ApMat gene to provide rapid, specific, and reliable molecular detection of C. fructicola, C. gloeosporioides, C. siamense, and C. cangyuanense, respectively. The data also provided a reference solution for the identification of species within Colletotrichum gloeosporioides species complex (CGSC), which share similar morphological characteristics. © 2022 Society of Chemical Industry.