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Cassava and yam plants are important staple foods of millions of people in the tropical world and provide food security in most parts of sub-Saharan Africa. Their production however is affected by anthracnose disease caused by Colletotrichum gloeosporioides, (Penz.) Penz. and Sacc contributing to 30-70% economic loss in both crops. A study was carried out to determine if variations exist between isolates of C. gloeosporioides on the two crops occurring in different agro-ecological zones of Ghana.  Anthracnose-diseased samples of cassava and yam plant parts (leaves and stem/vine) were collected from four agro-ecological zones of Ghana (Forest, Forest-Savannah Transition, Guinea and Coastal Savannah). Isolations of the causal organism C. gloeosporioides were made. The isolates were investigated on the basis of growth characteristics on Potato Dextrose Agar (PDA): presence or absence of setae, colour of cultures, dimensions of conidia. Pathogenicity of isolates was determined and molecular analysis conducted using Random Amplified Polymorphic DNA (RAPD). Results showed both similarities and variations in cultural, morphological and growth characteristics of the pathogen. Isolates from yam caused pathogenic lesions on cassava and yam plant sections and vice versa.  Forty-four isolates of C. gloeosporioides from cassava and yam compared by RAPD analysis grouped the isolates into three main clusters. Within two of the clusters are six polymorphic sub-groups relating to host and geographical origin. The different polymorphic sub-groups indicated that there are several sub-populations of C. gloeosporioides isolates, which either singly or in association, involved in the yam and cassava anthracnose infections in the field. Isolates from different ecological zones, with similar morphological features, clustering in a polymorphic sub-group suggest a common origin for some of them.