Fish assemblage of total 325 of Korean peninsula estuaries were surveyed to analyze the characteristics of community structure and diversity by sea areas for three years from 2016 to 2018. The scale (stream width) of Korean estuaries were various (14~3,356 m), and 68.9% of all estuaries showed salinity of less than 2 psu. Total 149 species classified into 52 families of fish were identified, and the dominant and sub-dominant species were Tribolodon hakonensis (relative abundance, RA, 12.5%) and Mugil cephalus (RA, 9.5%), respectively. The estuary of the Korean Peninsula had different physical and chemical habitat environments depending on the sea area, and accordingly, fish community structure also showed statistically significant differences (PERMANOVA, Pseudo-F=26.69, P=0.001). In addition, the NMDS (nonmetric multidimensional scaling) results showed the patterns that indicating fish community difference by sea areas, even though low community similarity within sea area (SIMPER, 21.79~26.39%). The estuaries of east sea areas were distinguished from the others in the aspects of which, the higher importance of migratory fishes and endangered species, and that of brackish species were characterized at south sea estuaries. However, the estuaries of west sea showed higher importance of species that have a relation with freshwater (primary freshwater species, exotic species), which is the result that associating with the lower salinity of west sea estuaries because of the high ratio of closed estuaries (78.2%). The SIMPER analysis, scoring the contribution rates of species to community similarity, also showed results corresponding to the tendency of different fish community structures according to each sea area. So far, In Korea, most studies on fish communities in estuaries have been conducted in a single estuary unit, which made it difficult to understand the characteristics of estuaries at the national level, which are prerequisite for policy establishment. In present study, we are providing fish community structure characteristics of Korean estuaries in a national scale, including diversity index, habitat salinity ranges of major species, distribution of migratory species. We are expecting that our results could be utilized as baseline information for establishing management policies or further study of Korean estuaries.