Fermented fish paste, an important source of cheap protein in some regions, is one of the most consumed condiments in the Philippines. Two species of fish, dilis (Stolephrus commersonii) and galunggong (Decapterus macrosoma) were subjected to irradiation as pretreatment method prior to production of bagoong isda. Pre-treatment at 3 and 10 kGy resulted in lower microbial load of the fermented fish paste. Irradiation of dilis resulted in an improved proteolytic degradation as compared with galunggong. There was no significant change in pH for both species. Acceptability scores of treatment at 3 kGy showed general improvement in the quality of the fish paste for dilis but not for galunggong. However, at 10 kGy, sample texture and overall acceptability was generally lower for dilis. SDS-PAGE electrophoresis of the water-soluble proteins indicate that at higher dose of radiation, fish proteins may have been converted to higher molecular weight aggregates which has affected fermentation properties of the substrates. Irradiation of fish prior to fermentation may result to chemical changes in proteins such as fragmentation, cross-linking, aggregation and oxidation and may likewise affect the chemical nature, physical state and organoleptic property of the final product.