In the last five decades, there has been a consistent decline in the total catch of fisheries in the Korean jurisdiction since the peak in 1986. The decline in catch slowed and slightly rebounded in the 2000s, but changed back to a decline in the 2010s. As indicators that can identify changes in the marine ecosystem, trophic level (TL), biodiversity index (H'), and the ratio between pelagic fish and demersal fish (P/D) were analyzed by each local marine ecosystem. There were some different changes in each local marine ecosystem, but the mean TL and H' decreased and P/D increased in general in Korean waters. Demersal fish, which were dominant in the 1970s and 1980s, declined, and small pelagic fish and cephalopods have dominantly changed since the 1990s. However, these changes are not simple, and they are fluctuating in complex ways relating to each marine ecosystem and the timing. It is believed that changes in marine ecosystems in Korean waters are likely caused by a combination of fisheries and climate change. The ecosystem indicators reflected a change in the total catch, a sharp drop in catch of demersal fish, and increasing catch of pelagic fish since the mid-1980s.