Cnaphalocrocis medinalis (Lepidoptera: Crambidae) is an economically important rice pest in Taiwan. The population genetic structure of C. medinalis is not clear and thus was studied in this research. Cnaphalocrocis medinalis samples were collected from six sampling locations in Taiwan using white sticky paper traps coated with sex pheromone. Genetic diversity was analyzed by mitochondrial and nuclear markers. Phylogenetic analysis revealed that all specimens of C. medinalis in Taiwan belonged to a single clade. Population genetic analysis of C. medinalis indicated no significant population structure because of a lack of significant genetic differentiation among the six sampling sites. Population genetic analysis also revealed no significant genetic differentiation among C. medinalis populations in Taiwan and neighboring regions, suggesting a common origin. The extremely low genetic diversity of C. medinalis in East Asia might be due to a population expansion after a recent founder effect. This study provides molecular information for understanding the population genetic structure of C. medinalis in Taiwan and East Asia.