Licania tomentosa (Chrysobalanaceae), also known as “oiti,” is a forest tree mainly used for urban afforestation in Brazil. Although anthracnose caused by Colletotrichum gloeosporioides is the main disease that threatens this tree, the identification of the species was based on morphological characteristics only. Owing to the need to use the molecular approach to pinpoint the identity of this pathogen with precision, the aim of this study was to identify endophytic and pathogenic Colletotrichum isolates from L. tomentosa based on both morphological and molecular data. For prior identification, partial sequences of the GAPDH region were obtained of all the 35 isolates (10 endophytic and 25 pathogenic). After analysis, ten isolates, representative of each clade, were selected for multilocus phylogenetic analysis (ACT, CAL, CHS‐1, GAPDH, TUB2, SOD2 and ITS). In addition, a tree based on the ApMat region was obtained for comparison with the multilocus tree. Morphological characterization (colony growth, conidial size and appressoria shape) was also performed for each species. To prove pathogenicity, L. tomentosa leaves were inoculated on the adaxial surface by mycelial plugs and conidial suspension. All isolates obtained belong to the Colletotrichum gloeosporioides complex. The Apmat tree has the same topology as the multilocus tree, allowing for the discrimination of the different species of Colletotrichum on L. tomentosa. Endophytic isolates of C. fructicola, C. queenslandicum, and C. siamense were acquired whereas pathogenic isolates were identified as C. siamense and C. tropicale, although all species were pathogenic on the wounded leaves of L. tomentosa. This is the first worldwide report of this Colletotrichum species associated with L. tomentosa and the first recording of C. queenslandicum in Brazil.