Anguillids are а valuable fish commodity worldwide. Although Anguilla luzonensis have been abundantly found in the northern Philippines and collected for trade, no available records show that it recruited in the mid-part where Lagonoy Gulf, Bicol is situated. In this study, we investigated the occurrence of A. luzonensis in the tributaries along the Lagonoy Gulf, Philippines using molecular tools. Glass eel specimens were collected in 2018–2019 from the Comun river, Albay; the Lagonoy river, Camarines Sur; and the Bato river, Catanduanes. For the first time, A. luzonensis was identified by molecular analysis in the Lagonoy Gulf. A. luzonensis was the second most abundant species in the Comun and Lagonoy rivers (9.5 and 22.4 %, respectively). Anguilla luzonensis collected from the Comun and Lagonoy rivers did not show a significant difference (FST= 0.00825, p>0.05). Anguilla marmorata was the most dominant species in all tributaries (71.1–98.0 %). In the Comun and Lagonoy rivers, A. bicolor pacifica was the third most abundant species (7.7 and 6.5%, respectively). In addition, Anguilla celebesensis was only found rarely in the Comun river (0.9 %). This study provides important information for sustainable resource management and effective utilization of the eel species in these regions.