The endangered kokako Callaeas cinerea wilsoni (Callaeidae), an endemic forest-dwelling passerine of New Zealand, has declined over the last century to a number of small isolated populations due to widespread habitat clearance and predation by introduced predators. To evaluate the genetic consequences of inbreeding and genetic drift, we examined genetic variability within and among 3 of the major remaining kokako populations using 4 polymorphic microsatellite loci. The largest remaining kokako population in the Te Ureweras was shown to have greater variability than the smaller Mapara and Rotoehu populations. Differentiation among the populations was low to moderate. We suggest there is no genetic barrier to translocations between the populations and that translocations of some individuals between the remaining kokako populations could enhance genetic variability of small populations to levels found in larger populations (e.g. Te Ureweras).