Recognizing the importance of the indigenous Philippine cultivars of Musa balbisiana Colla, which include the popular Saba varieties, it is essential to correctly identify these cultivars for various applications. Simple sequence repeat markers were used to generate DNA fingerprints and characterize the genetic diversity among 13 Philippine Musa balbisiana Colla cultivars and 5 other banana cultivars. Fifty-one primer pairs (45 from Musa and 6 from other species) were screened for PCR amplification and polymorphism across 18 cultivars. Fourteen primers were found to be polymorphic markers. A total of 49 alleles were generated, with a mean of 3.77 alleles per locus, ranging from 1-8 alleles. The resolving power of molecular markers measured as the Polymorphism Information Content (PIC) ranged from 0.23 to 0.80. Mean gene diversity ranged 0.08 to 0.49 indicating high density. The dendrogram using UPGMA-SAHN cluster analysis based on microsatellite polymorphism showed that the Saba cultivars clustered into two groups at 56% similarity level. Cluster analysis separated the cultivars of Musa balbisiana Colla from the other genotypes of Musa acuminate Colla and M. textilis. The 13 polymorphic SSR primers were shown to be able to identify and differentiate the 13 cultivars suitable for specific needs of the industry.