The genus Colletotrichum comprises an important and diverse group of endophytes, saprophytes and plant pathogens, many of which cause a syndrome known as anthracnose, on a wide range of hosts, mainly in tropical and subtropical regions. Since most of the accumulated research on the genus focuses on cultivated plants of commercial interest, the aim of this review was to explore how the genus has been studied in native woody plants in natural ecosystems. Following the PRISMA protocol for systematic reviews, we identified 52 original scientific publications that recorded Colletotrichum species associated with native woody hosts in natural environments in a taxonomic, ecological or phytosanitary context. Here, we conclude that research in natural ecosystems is scarce, mostly carried out in tropical areas and mainly focused on aspects of community ecology. We also observed the cosmopolitan nature of the genus, associated with many hosts, mostly as endophytes. The species most frequently recorded were in the ‘gloeosporioides’ complex, although due to the limitations in identification methods used in the studies, a large proportion of records could not be identified or verified at the species level.