In order to reveal the genetic subdivision within population of common wild rice Wza rufpogm Griff., allozyme analysis was conducted using 22 loci on a typical population from Yunnan Province, China. Non-random distribution of genotypes and/or genetic variability was found among three subpopulations, and the result was further demonstrated by considerable genetic differentiation observed (FsT= 0.206) within the population. Microhabitat selection may not be an important factor in shaping intra-population genetic structure, and restricted gene flow (fV,,,=0.964<1) and genetic drift act together towards a genetic subdivision within the population. This genetic subdivision may enhance inbreeding and will ultimately lead to genetic depletion within the predominantly outcrossing (t=0.830) perennial population, and therefore, more attention should be paid to the conservation and genetic management of the population.