BACKGROUND: This study was carried out to compare population size of mudfish (Misgurnus mizolepis) between the agricultural practices and to investigate the causes of its differences. We also provided basic information for sustainable use of mudfish population in paddy fields. METHODS AND RESULTS: Mudfish and benthic invertebrates which are diet of mudifish were investigated from 8 sites of organic and conventional rice paddy fields in South Korea. Total number of mudfish were 1,882 individuals in survey sites. Mudfish population were 2.4 times larger in organic paddy fields (1,333 individuals) than in conventional paddy fields (549 individuals). The population size of mudfish was larger in Mungyeong-si, Gyeongsangbuk-do and Anseong-si, Gyeonggi-do with relatively better environmental conditions than the other 5 sites including Suwon-si, Gyeonggi-do, Cheongyang-gun, Chungcheongnam-do, Gunsan-si, Jeollabuk-do, Gimje-si, Jeollabuk-do, Hwasun-gun, Jeollanam-do, Hamyang-gun, Gyeongsangnam-do. Benthic invertebrates collected from survey sites were 74 species, 68 genera, 46 families, 19 orders, 6 classes and 3 phyla. According to agricultural practices, benthic invertebrates were identified 66 species, 62 genera, 41 families, 17 orders, 6 classes and 3 phyla in organic paddy fields while there were 66 species, 60 genera, 42 families, 18 orders, 6 classes and 3 phyla in conventional paddy fields. Dominant invertebrates were Chironomidae sp., Branchiopoda sp., Ostracoda sp., and Copepoda sp. There were no differences in dominant species between organic and conventional paddy fields. Population size of mudfish tended to increase with the population size of Chironomidae sp., Branchiopoda sp., Ostracoda sp., and Copepoda sp. But, only population of Chironomidae sp. and Copepoda sp. statistically related to population size of mudfish. The number of individuals of mudfish (Misgurnus mizolepis) was higher at the low rate of urban area than any other surveyed region and was affected by appearance ratio of main preys such as Chironomidae sp. and Ostracoda sp. CONCLUSION(S): The population size of mudfish in rice paddy fields could be affected by environmental conditions and agricultural practices such as organic and conventional methods.