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Colletotrichum is the causal agent of anthracnose and other diseases on leaves, stems and fruits of numerous plant species, including several important crops. Accurate species identification is critical to understand the epidemiology and to develop effective control of these diseases. Morphologically-based identification of Colletotrichum species has always been problematic, because there are few reliable characters and many of these characters are plastic, dependent upon methods and experimental conditions. Rapid progress in molecular phylogenetic methods is now making it possible to recognise stable and well-resolved clades within Colletotrichum. How these should be reflected in a classification system remains to be resolved. An important step in providing a stable taxonomy for the genus is to epitypify existing names, and in so doing link them to genetically defined clades. We recommend a polyphasic approach to the recognition and identification of species within Colletotrichum, matching genetic distinctness with informative morphological and biological characters. This paper reviews various approaches in the study of Colletotrichum complexes including morphology, pathogenicity, physiology, phylogenetics and secondary metabolite production. A backbone phylogenetic tree using ITS sequence data from 42 ex-type specimens has been generated. \nPhylogenetic analysis using ITS sequence data is a useful tool to give a preliminarily identification for Colletotrichum species or place them in species complexes. However, caution must be taken here as the majority of the ITS sequences deposited in GenBank are wrongly named. Multi-gene phylogenetic data provides much better understanding of the relationships within Colletotrichum and should be employed where possible. We propose that an ideal approach for Colletotrichum systematics should be based on a multi-gene phylogeny, with comparison made with type specimens, and a well-defined phylogenetic lineage should be in conjunction with recognisable polyphasic characters, such as morphology, physiology, pathogenicity, cultural characteristics and secondary metabolites. Finally a set of protocols and methodologies is provided as a guideline for future studies, epitypification and the description of new species.