Captive populations are managed to promote demographic growth or stability and preserve genetic variation. Current protocols use survival rates to estimate the number of offspring needed to achieve target population size, while pedigree analysis is used to select breeding pairs to retain genetic diversity and minimize inbreeding. Despite these efforts, many captive populations fall short of programme goals. Reproductive failure of breeding pairs is a contributing factor, often as a result of pair incompatibility. Because choice is a component of most mating systems, providing a choice of mates could improve the sustainability of captive populations through increased fecundity and offspring survival while enhancing animal well-being. However, allowing mate choice might undermine genetic goals if those choices are inconsistent with genetic management objectives. Strategies for incorporating mate choice into management include: (1) using mate choice to increase reproduction of genetically valuable animals; (2) providing multiple genetically acceptable mates; (3) assessing mate preferences via odour or other cues before animal transfer; (4) using alternate breeding strategies, such as specialized breeding centres. Research is needed to determine whether incorporation of mate choice in breeding programmes can increase reproductive success without compromising genetic health and the potential to contribute to the conservation of wild populations.