The Golden-headed lion tamarin (Ghlt) is an endangered primate species, with a mandate from the Brazilian government for a genetically and demographically self-sustainable captive population with the primary role of assurance. The secondary roles are conservation education, research and fundraising. Assuming Ghlt founders are unrelated, the world captive population is large enough (about 520 individuals) to ensure conservation of 90% of gene diversity (GD) of the wild population for 100 years. It's current GD is 98% and 96% in the European (EEP) population. However, when taking into account founder relatedness (as estimated by molecular markers), this EEP estimate is reduced to about 86%. Using the same genetic markers, we also assessed GD in wild populations. Overall, the results suggest that these populations have a relatively low GD and high population genetic structure, raising questions about actual functional landscape connectivity. Assignment of captive animals to the wild subpopulations, suggests that captive animals may have originated from cross-breeding, resulting in relatively high GD compared to the wild. The continued loss of habitat makes it desirable to continue managing the self-sustainable world captive population as an insurance population. Future genetic research will further optimize this management in captive as well as wild populations.