Cacao (Theobroma cacao L.) is a tropical rainforest tree that is indigenous to the Amazon region of South America. The myriad of river basins present in the Upper Amazon are where the largest diversity of cacao populations is found. Although it is generally accepted that cacao was first cultivated in Mesoamerica, there is evidence for domestication in South America, the center of origin. “Piura Porcelana” is a traditional cacao variety from northern Peru that is cultivated for the gourmet chocolate market. The demand for fine-flavored cacao used in high-end chocolates and the corresponding premium prices paid for distinct cacao flavors provide economic incentives for the use and conservation of these traditional varieties. In the present study, we compared the genetic identity of Piura Porcelana cacao with 11 known cacao germplasm groups existing in the ex situ cacao genebanks, along with the living wild populations from the Santiago and Morona river valleys in northern Peru. The results of SNP analysis showed that Piura Porcelana shares the same general population membership with the “Nacional” cacao from Ecuador. However, Piura Porcelana significantly differed from Nacional (Fst = 0.185, P < 0.001), suggesting its unique genetic status. The high genetic similarity between Piura Porcelana and newly collected wild cacao suggested that the wild progenitors of Pirua Porcelana were from these river valleys, and this traditional variety could have been the result of independent domestication in northern Peru. These results provide new evidence of cacao domestication in the Amazon and will contribute to the sustainable use and conservation of these cacao genetic resources.