Tamarind is commonly grown as a subsistence crop to meet local needs. It is also commercially grown. Numerous national programs have identified tamarind as an underutilized crop with significant potential, owing to high product demand and the species' ability to be incorporated into agroforestry systems. This thesis generally aimed to assess the uniqueness of the reproductive parts of Tamarind (Taramindus indica Linn.) in various regions in Visayas Island in terms of its molecular and morphological propertics. Morphological characterization shows that the regions of Central Visayas possess the most unique traits among all regions in Visayas Island in terms of fruit parameters. The characterization also showed that leaves and flowers are not good indicators to differentiate sour tamarind fruits in Visayas. The primers for rbcL were successful in amplifying PCR products with success rates of a hundred percent and matK with negative result, Based on the analysis in molecular the researcher found out that rbcL produced 100% PCR (1/1) success rate and with matK primer produce 100% of PCR (2/2) success rate hence, the BLAST result showed that all the samples were 99.53% homologous. The closest present cultivar to the regions of Visayas with the reference to published accessions which formed a paraphyletic relationship in the tamarind under GenBank is the tamarind accessions of Phetchabun Province of Thailand. Keywords: molecular chracterization, morphology, tamarind, variability.