The design used to source animals for translocation and captive breeding programmes can strongly influence sampling results and outcomes. To date, no trapping design has been specifically directed at maximizing genetic diversity of individuals for use in such programmes. Using genetic and demographic data, we investigated the spatial structure of critically endangered woylie (Bettongia penicillata ogilbyi) populations for developing a spatial trapping design that would return a genetically representative cohort of animals by taking advantage of the dispersal behaviour of the species. Using microsatellite markers, we tested our design against more conventional trapping approaches and determined that animals captured under our spatial design were less related than animals captured using grid or standard transect designs. We clearly show that incorporating the target species’ ecology (e.g. dispersal patterns) in the capture design will improve the genetic differences (through reduced relatedness) between harvested individuals. This study sets out a practical approach that can significantly improve potential conservation outcomes. This approach is applicable to all species that have a predictable dispersal pattern.