In this study, we analyzed the fish species composition data of coastal capture fisheries in Taiwan between 1963 and 2010. The purpose of the analysis was to understand the long-term changes in marine ecosystems. A ratio-to-moving average method was used in conjunction with adjusted seasonal indices to determine the seasonality of individual catch items and to examine the trends shown by the species with the same seasonality. Over the 48-year timespan of the data, 31 species, i.e., 64% of the total number of species, were identified as seasonal migrants. The catch ratio for species showing a single peak in the spring increased steadily over time; however, those species with a single peak in the winter decreased. The catch ratio for those species with dual peaks in both summer and fall varied greatly before 1978. Increasing trends began in the 1980s and accelerated until 1998. As a result of this increase, the previous concentration of the fishing season in the winter months became highly diffuse. Additionally, the winter and/or spring species continued to decrease year after year as the summer and/or autumn species gradually came to dominate the catch. This change in fishing seasonality is likely not an anthropogenic effect. However, the change coincides with trends in sea surface temperature fluctuations. Such variation may not only cause structural change in marine ecosystems but can also significantly impact the economy and the livelihoods of those associated with the fishing trade.