The aim of this paper is to study the species composition, structure and seasonal dynamics of the cladoceran fauna and species associations in inland water bodies of Jeju Island (Republic of Korea). Only 47 taxa were found in 199 samples. Such faunal paucity could be explained by the existence of only a few types of aquatic environments on Jeju Island as compared to continental China and the Far East of Russia, with their great diversity of water types. We have demonstrated a high significance of the tropical species on Jeju. Our data confirm seasonal faunistic changes in the continental waters of Jeju Island. The rate of tropical taxa is highest in September, after the monsoon season, while the Far Eastern endemic taxa are more common in winter. At the same time, the contribution of Boreal taxa to the fauna of the island is low even in winter. Species associations have been revealed based on binominal distribution; they change significantly from summer to winter. However, a contribution of Boreal taxa to the species associations also is minimal (even in winter), whereas tropical taxa contribute to them greatly (including in winter). We can propose a rough scheme of faunal formation exploring the whole set of obtained information. Initially, at the earlier stages of the island formation, its fauna was consisted of some pre-Pleistocene taxa. Then, during the Pleistocene time, Jeju Island was secondarily interconnected with more southern territories, and tropical species have colonized it. Recent Boreal cladoceran invaders arrived at the island water bodies later when they were already inhabited by formed associations, and for this reason only few of them were able to settle down there. Such a scheme is a hypothesis which needs to be checked by the future phylogeographic studies.