To monitor changes of fish assemblage, we selected 5 study sites in lower-middle part of the Mankyeong (3 sites) and the Dongjin (2 sites) River, and conducted field sampling 2 to 4 times per year from 2007 to 2009. Total sampled fishes were 66 species in 16 families. Cyprinidae (RA, 73.25%; 33 species) was dominant family. Dominant species was Zacco platypus (RA, 19.96%), and subdominant species was Chelon haematocheilus (RA, 11.11%). There were 18 Korean endemic species (RA, 12.56%) and one endangered species, Liobagrus obesus, was only found in the Mankyeong River. Three exotic species were found: Carassius cuvieri, Micropterus salmoides and Lepomis macrochirus. Fish assemblages showed similar occurrence patterns around the sampling periods. As a result of species number comparison between before and after dike construction at MR1 and MR2, there was no huge difference. When fishes were classified into two types, primary freshwater and peripheral species, using habitat characteristics, number of primary freshwater species was increased from 14 to 21 after dike construction. Moreover, relative occurrence rate of primary freshwater species was increased to 53% compared with before construction (18%). On the other hand, number of peripheral freshwater species was decreased from 29 to 19 after dike construction. As a result of cluster analysis using Jaccard method, fish community before and after dike construction was distinguished each other.