Individual-based assignment tests are now standard tools in molecular ecology and have several applications, including the study of dispersal. The measurement of natal dispersal is vital to understanding the ecology of many species, yet the accuracy of assignment tests in situations where natal dispersal is common remains untested in the field. We studied a metapopulation of the grand skink, Oligosoma grande, a large territorial lizard from southern New Zealand. Skink populations occur on isolated, regularly spaced rock outcrops and are characterized by frequent interpopulation dispersal. We examined the accuracy of assignment tests at four replicate sites by comparing long-term mark-and-recapture records of natal dispersal with the results of assignment tests based on microsatellite DNA data. Assignment tests correctly identified the natal population of most individuals (65–100%, depending on the method of assignment), even when interpopulation dispersal was common (5–20% dispersers). They also provided similar estimates of the proportions of skinks dispersing to those estimated by the long-term mark-and-recapture data. Fully and partially Bayesian assignment methods were equally accurate but their accuracy depended on the stringency applied, the degree of genetic differentiation between populations, and the number of loci used. In addition, when assignments required high confidence, the method of assignment (fully or partially Bayesian) had a large bearing on the number of individuals that could be assigned. Because assignment tests require significantly less fieldwork than traditional mark-and-recapture approaches (in this study < 3 months vs. > 7 years), they will provide useful dispersal data in many applied and theoretical situations.