In support to policy formulation of fisheries in Agusan Marsh, a stock assessment was conducted for the period of May 2014 to December 2016 using the data collected from Lapaz and Talacogon, Agusan del Sur within the Agusan Marsh. Results showed that Lapaz contributed 54% of the catch over Talacogon. A total of eighteen species, belonging to 13 genera and 11 families with 7 native and 11 introduced species were found in the marsh. Majority of the total catch consisted of Channa striata, Oreochromis niloticus, and Cyprinus carpio (35%, 27%, and 26%, respectively). Osphronemus laticlavius, Glossogobius celebius and Mugil cephalus were listed as seasonal species. An invasive janitor fish (Pterygoplichthys disjunctivus) was observed as by-catch. A strong pattern of high catch rates occurred during the rainy months of January, February, June, and December. Ten types of commonly used fishing gears were found, majority of which include fish pots, set gillnets, electrofishing and set long lines. Multivariate analysis showed similarity in species composition both in Lapaz and Talacogon. Exploitation of dominant species showed unsustainable level for O. niloticus, C. batrachus, C. caprio, andC. gariepinus, mainly due to excessive capture of immaturesized fishes by major fishing gears. The estimated exploitation rate is beyond the optimum level for O. niloticus and C. carpio in both years and followed by C. striata and C. gariepinus in 2016. Only C. bartachus is estimated to be exploited below the optimum level. Generally, the key species in Agusan Marsh are at risk of overfishing, hence, immediate policy measures must be given high attention.