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In this study, we wanted to obtain the information of the ecological impact of alien species on native fish communities. The Ichthyofauna and fish community in Joongchosan Reservoir and Bukchosan Reservoir in Gunsan-si Korea were investigated over the period from March to October 2020. During the survey period, a total of 1,895 individuals representing eight species, five families, and four orders were caught in the Joongchosan Reservoir. In the Bukchosan Reservoir, a total of 171 individuals were caught, representing seven species, five families, and three orders. The dominant species and subdominant species of Joongchosan Reservoir were Pseudorasvora parva (661 individuals, RA: 34.7%), and Rhodeus ocellatus (660 individuals, RA: 34.7%). Conversely, Micropterus salmoides (77 individuals, RA: 45.0%), and Carassius auratus (60 individuals, RA: 35.1%), were the two most common species in the Bukchosan Reservoir. The community indices showed a dominance of 0.697, diversity of 1.483, evenness of 0.713, and species richness of 0.928 in the Joongchosan Reservoir. In comparison, the community indices in the Bukchosan Reservoir showed a dominance of 0.801, diversity of 1.304, evenness of 0.670, and species richness of 1.167. This study confirms that the number of native fishes and the associated community diversity have decreased due to the influence of Micropterus salmoides. This highlights the need for removal of alien species from reservoirs, while simultaneously preventing future introductions.