A collection of 40 Musa L. (Musaceae) accessions covering taxa of sections Eumusa, Australimusa, Callimusa and Rhodochlamys was used for analysing the molecular diversity of the genus. This collection includes cultivars and different wild species. The analysis utilized two PCR-based molecular marker systems, namely amplified fragment length polymorphism (AFLP) and sequence related amplified polymorphism (SRAP) that amplifies open reading frames. A total of 837 AFLP and 403 SRAP bands were generated using 15 AFLP and 10 SRAP primer combinations, of which 787 and 353 bands showed polymorphism, respectively. Both the unweighted pairgroup method of arithmetic average dendrogram and principle component analysis clearly separated the accessions in accordance to their sections and species. However, the percentage of polymorphism amongst sections and species, and the relationships within Eumusa species and subspecies varied between the two marker systems. The clustering of accessions with SRAP marker information was according to their phenotypic characteristics more than AFLP markers. From the total number of SRAP and AFLP amplified bands 29% and 13%, respectively, were specific and unique for certain sections and genotypes. Concerning the Eumusa, SRAP showed to be a valuable marker to discriminate amongst M. acuminata, M. balbisiana and M. schizocarpa, as well as between plantains and cooking bananas, which could be useful in Musa improvement.