Taiwan's marine fisheries were encountering the challenge of climate change, deterioration of the marine environment, and the decline of fishery resources. Climate change leads to rising sea water temperature, with the consequences of changing habitats, alteration of distribution boundary, and changing fishing grounds. The effect of climate change is profound for fishery resources and the characteristics of water masses are the key factors that affect the variation of fishing grounds and fishing season. As a result, Fisheries Research Institute implemented “Taiwan Cooperative Oceanic Fisheries Investigations (TaiCOFI)” program in 2003 to conduct cruises to collect water temperature, salinity, nutrients, chlorophyll-a and zooplankton measurements at 62 stations in the surrounding waters of Taiwan. Through this thorough investigation, we try to understand the coupling of physical, chemical and biological dynamics in the surrounding waters of Taiwan to figure out the factors associated with the fluctuation of fishery resources and to monitor our ocean and to detect anomalies effectively and to find a way to mitigate the impact of climate change.