The sequence related amplified polymorphism (SRAP) was used to assess genetic relationship among some Musa balbisiana related accessions including wild diploid, triploid cultivar, plantains, diploid and tetraploid hybrids. A total of 74 bands were generated, of which 65 bands (87.84%) were polymorphic among the tested accessions. The average of polymorphism information content (PIC) for all primers was 0.29, while the average of diversity index (DI) was 0.73. Results showed the SRAP efficiency in grouping the tested accessions and exposing minimum differences among genotypes. Interestingly, the wild diploid accessions were separated into two groups, in which BB-CICY, Tani, Cameron and Singapuri grouped together with the triploid cultivar “Lep Chang Kut”, while the other diploid accessions, i.e. Butuhan, Pisang Batu and BB-545, formed the second group near to plantains and hybrids. These findings were subsequently supported by the identification of some specific bands generated by SRAP, which were existed in all B genome contained accessions with the exception of Butuhan, Pisang Batu and BB-545. The results suggested that these accessions may have recombinant chromosomes of A and B genomes or they are mislabeled. The identification of the specific bands for B genome found in this study provided markers linked to chromosomes 2, 8 and 11, which could be helpful in discriminating banana and plantain cultivars. Specific primers were designed from sequences of some specific bands, among which a 256bp fragment was successfully amplified, and was able to distinguish between acuminata and balbisiana accessions. Moreover, the information herein could be important in Musa basic breeding program, identification of mislabeled accessions and germplasm management and conservation.