Many of the world's turtles and tortoises are currently threatened with population extinction. Some species are so threatened in their native habitats that the only way to ensure their survival may be through captive propagation, an endeavor in which many private conservation organizations are currently engaged. In this review we outline the genetic issues that need to be considered when establishing captive breeding colonies of tortoises and turtles for eventual reintroduction or population supplementation. The first section of this review stresses the importance of creating breeding units that are based on the population structure of a species in its native range. We discuss how molecular methods and the concepts of evolutionarily significant units (ESUs) can be used to define breeding units for captive breeding colonies and determine their geographic origin for reintroduction. In the second section we discuss the need to maintain the genetic variability of the colony members and the techniques that are available to achieve this goal.