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Genetic relationship among subspecies of Musa acuminata and A-genome consisting edible cultivated bananas was investigated by ISSR (inter-simple sequence repeat) markers. Twelve samples of wild type bananas that were classified into 5 subspecies of Musa acuminata, thirty-three samples of edible cultivatedbananas and M. balbisiana were used as plant materials for this study. Of a total of 36 ISSR primers screened, 6 primers revealed a total of 128 alleles, allele size varied from 200 to 3,000 bp with an average of 21.33 alleles per primer, average of allele frequency was 0.18, polymorphic percentage was 1.0 and heterozygositywas 0.29. From the dendrogram, banana samples can be divided into two main clusters with similarity coefficient value at 0.18. The first cluster belonged to the out group which included Musa itinerans and Ensete glaucum, the second cluster belonged to Musa coccinea, M. laterita, all subspecies of M. acuminata, M. balbisiana and all the cultivar groups of the edible cultivated bananas and plantains. In addition, the results indicated two Musa species, consisting of M. coccinea and M. laterita, were sister group of the second cluster as well. All specimens of subspecies of M. acuminata were related to cultivated groups of A-genome consisting of cultivated bananas in Thailand.