Description: A prominent increase in the moon jellyfish (genus Aurelia) populations has been observed since 1980 in two semi-enclosed temperate seas: the northern Adriatic Sea and the Inland Sea of Japan. Therefore, we reviewed long-term environmental and biotic data from the two Long-Term Ecological Research (LTER) sites, along with the increase in the moon jellyfish occurrence to elucidate how these coastal seas shifted to the jellyfish-dominated ecosystems. The principal component analysis of atmospheric data revealed a simultaneous occurrence of similar climatic changes in the early 1980s; thereafter, air temperature increased steadily and precipitation decreased but became more extreme. Accordingly, the average seawater temperature from March to October, a period of polyps' asexual reproduction i.e. budding, increased, potentially leading to an increase in the reproductive rates of local polyp populations. Conspicuous eutrophication occurred due to the rise of anthropogenic activities in both areas from the 1960s onwards. This coincided with an increase of the stock size of forage fishes, such as anchovy and sardine, but not the population size of the jellyfish. However, by the end of the 1980s, when the eutrophication lessened due to the regulations of nutrients loads from the land, the productive fishing grounds of both systems turned into a state that may be described as 'jellyfish-permeated,' as manifested by a drastic decrease in fish landings and a prominent increase in the intensity and frequency of medusa blooms. A steady increase in artificial marine structures that provide substrate for newly settled polyps might further contribute to the enhancement of jellyfish population size. Elevated fishing pressure and/or predation by jellyfish on ichthyoplankton and zooplankton might jeopardize the recruitment of anchovy, so that the anchovy catch has never recovered fully. These semi-enclosed seas may represent many temperate coastal waters with increased anthropogenic stressors, which have degraded the ecosystem from fish-dominated to jellyfish-dominated.