Small island populations are particularly prone to extinction due to the effects of genetic drift and inbreeding reducing genetic variation and fitness of such populations. Furthermore, isolated island populations may experience population divergence due to drift or divergent selection. Reciprocal translocations of individuals between populations may be used to stimulate gene flow between such isolated populations. To determine whether populations of the endangered Chatham Island black robin Petroica traversi may benefit from such translocations, we compared levels of genetic diversity and differentiation within and among populations of the black robin and its sympatric sister-species, the Chatham Island tomtit Petroica macrocephala chathamensis. Although the black robin has recovered following a severe population bottleneck, the bottleneck and subsequent intense inbreeding experienced by the black robin have likely had long-term consequences affecting the viability of this endangered species. We analysed the genetic diversity and population structure of the black robin at 15 polymorphic microsatellite loci, and compared this to the level and pattern of genetic diversity from 17 polymorphic loci for the tomtit, which comprises three larger island populations. The black robin displayed a lower number of alleles and expected heterozygosity than the Chatham Island tomtit. We also found that island populations of both species have differentiated from one another, likely due to strong genetic drift acting independently on these populations over a period of isolation. Reciprocal translocations of black robins between islands are recommended to prevent further loss of diversity through drift, and so to improve the probability of species persistence.