We compare the performance of Nm estimates based on FST and RST obtained from microsatellite data using simulations of the stepwise mutation model with range constraints in allele size classes. The results of the simulations suggest that the use of microsatellite loci can lead to serious overestimations of Nm, particularly when population sizes are large (N > 5000) and range constraints are high (K < 20). The simulations also indicate that, when population sizes are small (N ≤ 500) and migration rates are moderate (Nm ≈ 2), violations to the assumption used to derive the Nm estimators lead to biased results. Under ideal conditions, i.e. large sample sizes (ns ≥ 50) and many loci (nl ≥ 20), RST performs better than FST for most of the parameter space. However, FST-based estimates are always better than RST when sample sizes are moderate or small (ns ≤ 10) and the number of loci scored is low (nl < 20). These are the conditions under which many real investigations are carried out and therefore we conclude that in many cases the most conservative approach is to use FST.