Abstract Despite its significance in evolutionary and conservation biology, few estimates of effective population size (Ne) are available in plant species. Self-fertilization is expected to affect Ne, through both its effect on homozygosity and population dynamics. Here, we estimated Ne using temporal variation in allele frequencies for two contrasted populations of the selfing annual Medicago truncatula: a large and continuous population and a subdivided population. Estimated Ne values were around 5–10% of the population census size suggesting that other factors than selfing must contribute to variation in allele frequencies. Further comparisons between monolocus allelic variation and changes in the multilocus genotypic composition of the populations show that the local dynamics of inbred lines can play an important role in the fluctuations of allele frequencies. Finally, comparing Ne estimates and levels of genetic variation suggest that He is a poor estimator of the contemporaneous variance effective population size.