Taramindus indica L., commonly known as "Sampalok" in the Philippines, is a tropical fruit recognized for its delicate flavor that may contribute to the worldwide market. In the Philippines, there are two (2) varieties of tamarind: sweet and sour. However, it is difficult to identify which is sour and which is sweet when they are seedlings. This study aimed to implement morphology and molecular characterization on the reproductive parts of tamarind from Mindanao; assessed morphological characteristics of reproductive parts of tamarind using Taxonomic Keys; amplified the regions of tamarind using rbcL and matK DNA marker; and, determined the relationships of samples per region using Phylogenetic Analysis. The results of the morphological characterization indicate that the leaves are almost the same but varied in leaf apex shape; with the flowers, the colors of their buds having red streak, petals, and calyx exhibits the difference between samples; and with the fruits of Mindanao, all gathered data share a common fruit shape, fruit apex. It shows that fruits from Butuan City were the longest among the samples. BLAST results show that Mindanao cultivars were comparable with the sequences available of Tamarindus indica with outgroups having 98-100% similarities. The rbcL DNA primers appeared to have the best findings for the tamarind collection in Mindanao. Cagayan de Oro and Butuan formed a monophyletic relationship as well as Davao City and Maguindanao City. They formed a paraphyletic relationship with the Thailand tamarind. Hence, it was concluded that these two (2) markers (matK and rbcL) could be used for the molecular identification of tamarind from Mindanao. It also shows that the tamarind samples from Mindanao have a close relationship with Thailand's Priao-yak Province. Keywords: Tamarind, morphology, DNA barcoding, cultivars, relationship.