Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short and long term persistence of populations and species. However, the relative spatio-temporal impacts of translocations on neutral and functional genetic diversity and how this affects genetic structure among the conserved populations overall has received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC) class I diversity over a 23-year period in the Seychelles warbler (Acrocephalus sechellensis). We found low and stable microsatellite and MHC diversity in the source population and evidence for only a limited loss of either type of diversity in the four new populations. However, we found evidence of significant, but low to moderate, genetic differentiation between populations with those populations established with fewer founders clustered separately. Stochastic genetic capture (as opposed to subsequent drift) was the main determinant of translocated population diversity. Further, a strong correlation between microsatellite and MHC differentiation suggested that neutral processes outweighed selection in shaping MHC diversity in the new populations. These data provide important insights into how to optimise the use of translocation as a conservation tool.