The detection of reductions in effective population size (Ne) or census size (Nc) is essential for conservation. Recent developments allow wildlife researchers to obtain genetic material via non-invasive sampling techniques that may provide the large sample sizes necessary for precise estimates of Ne and Nc. Population genetic theory provides several methods to estimate Ne from allele frequency data: including temporal change in allele frequencies, gametic disequilibrium and heterozygote excess methods. Modification of capture–mark–recapture methods for use with multi-locus genotype data provides new means for estimating Nc. The combination of new DNA sampling techniques, polymerase chain reaction-based DNA markers and analytical methods may provide unprecedented power to detect reductions in Ne and Nc of endangered populations. However, these genetic methods are largely untested in the field. We review some relatively unexplored, but promising ways that multi-locus genetic data can be used to provide important genetic and demographic information and suggest avenues for further research in this area.