The spatial genetic structure within a population of an endangered plant, Cerastium fischerianum var. molle, was examined using spatial autocorrelation analysis. All individuals in 22 x 15 m area in a population were mapped and genotyped by three allozyme loci. Many spatial autocorrelation indices (Moran's I) were significantly larger than the expected values and their averages across three marker loci examined were positive in the short distance classes and the opposite pattern was shown in the larger distance classes, suggesting that individuals located nearly each other tend to have similar genotypes and pairs of individuals located far from each other tend to have different genotypes. Because the marker loci are considered to be neutral and the linkage disequilibria were not detected, the spatial genetic structure observed in this study seems to result from the restricted gene flow because of predominant selfing of C. fischerianum var. molle.