Paddy fields are important habitats for maintaining the biodiversity of agricultural ecosystems. Recently, as the need for safe food and biodiversity conservation has increased, the rice cultivation methods have undergone changes. This study was conducted to investigate the fish fauna in Environmentally Friendly Paddy fields (EFP) and Conventional Paddy fields (CP), and compare the characteristics of Misgurnus anguillicaudatus and Aphyocypris chinensis populations in EFP and CP. A total of 2,703 fish were collected and classified into six families and 13 species. Our results showed that there was a difference in the proportion of fish populations in the two paddy fields, and the number of individuals in EFP was higher than in CP. The weight values of M. anguillicaudatus were higher in EFP than in CP, and the total length, body length, and weight values of A. chinensis were higher in EFP than in CP. Conditional factor (K) values also showed similar trends in EFP and CP. Our results indicate that the farming practices in paddy fields have a significant effect on the characteristics of M. anguillicaudatus and A. chinensis populations, and the results of this study can be used as basic data for securing biodiversity in future agricultural ecosystems.