Paragonimus westermani is a food-borne zoonotic trematode transmitted to humans through the consumption of undercooked crustaceans. Freshwater crabs act as the second intermediate host for the encysted metacercariae stage. However, accurate identification of intermediate hosts remains a challenge. Here, we aimed to detect and identify P. westermani in randomly collected freshwater crabs and determine the species of infected crabs in Davao Oriental through molecular methods. Specifically, Sanger and next-generation sequencing were conducted for species identification through BLASTn, followed by phylogenetic analyses to understand geographic and taxonomic relationships. Results showed P. westermani DNA was detected in five out of eleven crab samples and these sequences were closely grouped to the Philippine reference sequence. Through a similar approach, the infected crabs showed high sequence similarity and formed tight clustering to Isolapotamon sp. Overall, the results provided evidence that P. westermani DNA was detected in Isolapotamon sp., a genus endemic to Mindanao, and can be a potential intermediate host. This expands our current understanding of transmission ecology beyond the only known intermediate host in the Philippines, Sundathelphusa philippina.