This paper investigates the relationship between retail and wholesale prices of milkfish (Chanoschanos), tilapia (Tilapianilotica), and tiger prawn (Peneaus monodon) using techniques that recognize the role of seasonal factors for testing orders of integration of and the existence of cointegration between these prices. This paper finds that seasonality plays an important role in explaining movements in the prices of these farmed species. This is so because, with the exception of the wholesale price of tiger prawn, unit roots occur at all frequencies for all of the prices that were examined. None of the pairs of prices were found to be cointegrated at all frequencies. However, the retail and wholesale prices of tilapia were found to be cointegrated at zero and annual frequencies. These findings suggest that regressions on the levels of retail and wholesale prices of milkfish and tiger prawn could lead to spurious results. Hence, price formation based on level of prices for these two aquaculture species can send wrong signals to the market stakeholders, i.e., producers, middlemen, and consumers.