The fishing grounds of Korean large-pair trawlers have shifted since exclusive economic zones (EEZs) were established in a fisheries agreement involving countries neighboring Korean waters. The distributions of marine ecosystems and fisheries resources have been changing with environmental changes such as global warming and with the shift in species targeted as a result of changes in fishing technology and fishing gear. This study analyzed variation in the species assemblages caught in Korean waters by large-pair trawlers as a result of these geopolitical and environmental changes. The data used in this study were obtained from the Fishery Production Statistics of Korea and the Port Sample Survey of the National Fisheries Research and Development Institute (NFRDI) from 1990 to 2007. Hierarchical clustering analysis (HCA) and correspondence analysis (CA) were used to explore the characteristics of the catch-species composition. The overall variation in the species composition of the catch of Korean large-pair trawlers showed that the proportions of croaker Johnius grypotus, small yellow croaker Larimichthys polyactis, eel Anguilla japonica, and blue crab Portunus trituberculatus decreased, whereas those of hairtail Trichiurus lepturus, Spanish mackerel Scomberomorus niphonius, anchovy Engraulis japonicus, and common squid Todarodes pacificus increased in Korean waters over the 18-year period. The results of the HCA of the annual catch data by species showed four different distributions of fish species according to year. Results of the CA showed that the species assemblages differed between the 1990s and 2000s.