Forty Colletotrichum musae isolates were recovered from ten different banana cultivars (Musa spp.) exhibiting the symptoms of both crown rot and anthracnose. The isolates were characterized morphologically and with molecular tools. Based on morphological characters in culture, the 40 C. musae isolates were included in four groups. Group I consisted of fast growing isolates with pinkish to light orange mycelia; group II included isolates with sparse, slow growing, suppressed, light orange mycelia; group III consisted of isolates with dense, fast growing, orange mycelia; and group IV included isolates with profuse cottony mycelia, mostly white to very light orange colour. Twelve isolates of C. musae were further selected and tested with RAPD primers for their genetic diversity. The RAPD dendrogram grouped the 12 isolates of C. musae in three clusters. Based on RAPD patterns, the similarity index (SI) within C. musae isolates ranged from 41.66 to 100%. Thus, the RAPD analysis revealed a high genetic variability in C. musae isolated from different banana cultivars. This might explain the differences in cultural characteristics of different isolates.