Ardisia crenata Sims, one of the most widely distributed Ardisia in the world, is an important ornamental and medicinal plant species. Using 7 polymorphic nuclear microsatellite loci, we studied the genetic variation of 20 natural populations of A. crenata across its distribution centre, the south China. Significant deviation from Hardy-Weinberg equilibrium in all populations and at all loci were detected, and the fixation index was high (FIS = 0.725), indicating that inbreeding may be dominant in the mixed mating system of this self-compatible species. The average genetic diversity within populations was relatively low (HS = 0.321). There was significant genetic differentiation among populations (FST = 0.583), which may be resulted from high level of inbreeding and low level of gene flow. A. crenata in south China can be roughly divided into eastern group and western group, consistent with the floristic division of Sino-Himalayan forest subkingdom and Sino-Japanese forest subkingdom. It was suggested that there may be separated glacial refugia in each region.