Using RAPD markers and one morphological marker, we studied the among- and within-population structure in a selfing annual plant species, Medicago truncatula GAERTN. About 200 individuals, sampled from four populations subdivided into three subpopulations each, were scored for 22 markers. It was found that the within-population variance component accounted for 55% of the total variance, while the among-population variance component accounted for 45%. Eighteen percent of the total variance was due to within-population structure (i.e., among subpopulations). Thus, 37% of the total variance was within subpopulations. Using a multilocus approach, it was found that no multilocus genotype was common to two populations. Two of the four studied populations were composed of few (less than or equal to 6) multilocus genotypes, whereas the other two had many (greater than or equal to 15) multilocus genotypes. In the most polymorphic population (37 genotypes), only one genotype was found to be common to two subpopulations. Resampling experiments show that, depending on the population, three to 16 polymorphic loci were necessary and sufficient to score all multilocus genotypes in the population. When these data are compared to published results, it appears that on some occasions, the number of genotypes per population of selfing species might be larger than would be expected from the sole consideration of effective population size. The large within-subpopulation genetic variance observed in some populations could be explained by either small neighborhood sizes within subpopulations, or by outcrossing following migration through seed and/or pollen.