There are relatively few studies on parasite fauna of marine fishes in Philippine waters. This study aimed to determine the prevalence of marine ascaridoid infection in species in Balayan Bay and Tayabas Bay. A total of 371 fishes belonging to three different species of ( [ = 130], [ = 121], and [ = 120]) were collected. Ascaridoid parasite larvae were found in all fish host species, with an overall fish infection rate of 22%. The highest infection rate was observed in (27.69%), followed by (19%), and then (17.50%). Moreover, a higher prevalence of infection was detected in Tayabas Bay (27.57%) than in Balayan Bay (15.59%). Molecular analyses based on the and gene supported the identification of the larvae into two species: and () . This is the first report of the genetic identification of these two helminth parasites in fish species in the Philippines. Paucity in the database of Philippine marine fish parasites warrants more research efforts, especially concerning economically important fish species with implications to food safety and food security.