The growth of the aquaculture sector had evolved to be an important source of expansion in Philippine fisheries, and the total agricultural sector as a whole. To date, it is one of the few food sectors in the country where net exports are positive. This paper attempted to identify the major sources of productivity growth in the four largest farmed species in the country, i.e., milkfish, tilapia, tiger shrimp and seaweeds. The study employed the Tornqvist TFP (total factor productivity) decomposition analysis to measure the growth in nominal revenue and cost of production of the respective species, in terms of output growth, inflation in both output and input prices and intensification in input use. Results of the study showed that the annual growth in total factor productivity (TFP) ranged from 28 to 82 percent with the higher TFP growth rates being contributed by the seaweeds and milkfish sector, while lower shares were registered in tilapia and tiger prawn aquaculture. Moreover, the paper investigated the factors that helped foster output growth such as R&D, credit and infrastructure developments to determine their respective roles in the growth of the aquaculture sector in the country.