Wild radish (Raphanus sativus L. var. hortensis f. raphanistroides Makino) is widely distributed in East Asia; however, its genetic diversity and population structure remain poorly understood. In our study, DNA sequence and microsatellite loci were used to analyze wild radish populations across the whole East Asia. Population genetic diversity analysis showed thatthe East Asian wild radish populations generally had high genetic diversity (average H_O=0.448), distinct population structure, and a positive correlation between genetic distance and geographic distance. AMOVA analysis suggested the genetic diversity among individuals in populations by far exceeded the diversity among populations/groups. The outcrossing breeding system, long geographic distance between populations and gene flow from cultivated radish populations may explain the high level of genetic diversity within wild populations. Bayesian cluster analysis identified four genetic clusters in the East Asian wild radish populations, observed by DNA sequencing analysis. The possible factors would be various aspects, such as oceanic barrier, climate fluctuations, and pollinators’ characteristics. This study provides a reference for the utilization of wild radish germplasm resources and the improvement of radish varieties in East Asia.