Indirect genetic methods are frequently used to estimate the effective population size (Ne) or effective number of breeders (Nb) in natural populations. Although assumptions behind these methods are often violated, there have been few attempts to evaluate how accurate these estimates really are in practice. Here we investigate the influence of natural selection following a population admixture on the temporal method for estimating Ne. Our analytical and simulation results suggest that Ne is often underestimated in this method when subpopulations differ substantially in allele frequencies and in reproductive success. The underestimation is exacerbated when true Ne and the fraction of the low-fitness group are large. As an empirical example, we compared Nb estimated in natural populations of steelhead trout (Oncorhynchus mykiss) using the temporal method (N̂b[temp]) with estimates based on direct demographic methods (N̂b[demo]) and the linkage disequilibrium method (N̂b[LD]). While N̂b[LD] was generally in close agreement with N̂b[demo], N̂b[temp] was much lower in sample sets that were dominated by nonlocal hatchery fish with low reproductive success, as predicted by the analytical results. This bias in the temporal method, which arises when genes associated with a particular group of parents are selected against in the offspring sample, has not been widely appreciated before. Such situations may be particularly common when artificial propagation or translocations are used for conservation. The linkage disequilibrium method, which requires data from only one sample, is robust to this type of bias, although it can be affected by other factors.