Conservation uses information from genetics to assist in management decisions. However, conservation genetics typically assesses genetic diversity at the DNA level but this alone does not address all the risks associated with managing wild and captive populations. DNA is packaged into chromosomes. Differences in the number and morphology of chromosomes between species or even between populations of the same species can have important implications for management programs for threatened species. Cytogenetics, analysis of the higher molecular chromosome structure, can provide invaluable insight for the management of threatened species, where DNA alone could not address all genetic risks and threats to populations. Here we outline the important and valuable role of cytogenetics in conservation, highlighting two case studies based on threatened Australian marsupials: rock-wallabies and the Tasmanian devil. In conclusion, we summarise how cytogenetics should be better linked to conservation genetics and integrated into our management of threatened species, to ensure they have the best platform from which to persist and adapt into the future.