Simple sequence repeat (SSR) or microsatellite markers were identified for Philippine varieties of papaya for varietal identification, diversity analysis, and hybridity assessment. Fourteen SSR markers were screened using PCR for amplification and polymorphism. Six primer combinations namely, CPMET, BGAL, ACC, CPY, SSR 12 and SSR 35, were effective in fingerprinting and diversity analysis and for hybridity testing, except for CPMET. The genetic relationship of the selected papaya varieties was established based on UPGMA clustering. At 0.76 coefficient of similarity, three groups were observed, namely: Group I (Davao Solo, Maradol and Red Lady), Group II (Sinta and Cavite Special) and Group III (Morado). The heterozygosity of each locus varied from 0.38 to 0.57 with an average of 0.51. ACC, BGAL and SSR 35 markers were predominated by major alleles with ≥ 75 percent. Distinct DNA fingerprints were obtained for the six papaya cultivars, the transgenic papaya lines, backcross lines, recurring parent and hybrids. For hybridity testing, the SSR markers CPY, BGAL, SSR 12 and SSR 35 were able to discriminate the F₁ hybrid and its parents. This study shows that the identified SSR markers are effective in analyzing diversity, providing definitive fingerprints and testing hybridity. Key words: SSR, microsatellite markers, molecular markers, papaya, DNA fingerprints, genetic diversity analysis, hybridity testing