Marine spatial planning (MSP) has been proposed to facilitate the sustainable use of oceans. To implement MSP in coastal zones, we need to understand the current status of aquaculture, in order to plan for its future. In Japan, coastal aquaculture is based on fishery rights, but it is hard to establish the existing situation as there are so many aquaculture facilities in place. In this study, we used full polarimetric, L-band PALSAR-2 data to identify aquaculture areas. We calculated HH and HV backscattering coefficients, and applied polarimetric decomposition analysis to three-component scattering models. The HV backscattering coefficient successfully discriminated aquaculture areas from the sea surface, while the HH backscattering coefficient was mostly able to discriminate between raft and longline aquaculture areas. The three-component scattering model was then able to discriminate between raft and longline aquaculture types in areas where the HH backscattering coefficient could not. Weather conditions affected the sea surface and therefore influenced the outcomes of our analyses.