Phyllosticta citriasiana is the causal agent of citrus tan spot, an important pomelo disease in Asia. At present, there is little or no information on the epidemiology or population structure of P. citriasiana. Using simple sequence repeat (SSR) markers, 94 isolates obtained from three pomelo production regions in southern/southeastern China were analyzed. The analyses showed high genetic diversity in each of the three geographic populations. A STRUCTURE analysis revealed two genetic clusters among the 94 isolates, one geographic population was dominated by genotypes in one cluster while the other two geographic populations were dominated by genotypes of the second cluster. P. citriasiana has a heterothallic mating system with two idiomorphs, MAT1-1 and MAT1-2. Analyses using mating type-specific primers revealed that both mating types were present in all three geographic populations, and in all three populations the mating type ratios were in equilibrium. Although the sexual stage of the fungus has not been discovered yet, analyses of allelic associations indicated evidence for sexual and asexual reproduction within and among populations. Despite the observed genetic differentiation among the three geographic populations, evidence for long-distance gene flow was found.