I discuss future challenges and opportunities in genetic approaches to biodiversity conservation. Resolving taxonomy uncertainties and identifying diverged evolutionary units within species are both bedevilled by a plethora of definitions: the challenge for the conservation community is to come to an agreed definition of species and for a unit within species for conservation purposes. For genetic management in the wild, the main challenge is to apply well-established genetic principles to management, especially of fragmented populations. Fears about outbreeding depression are preventing rational use of gene flow for genetic rescue; predicting the risk of outbreeding depression is the most important unmet scientific challenge in the field. The major challenge in genetic management of captive populations of threatened animal species is to institute explicit management to minimize genetic adaptation to captivity, so that reintroduction success is maximized. The development of low cost genome sequencing offers many research opportunities and challenges. For example, there are opportunities to identify genes involved in speciation and a major challenge is to devise molecular tests to predict reproductive isolation between populations. Genomics offers opportunities to provide higher precision estimate for many parameters of importance to conservation. A major challenge is to devise means to assess, on a genome-wide basis, genetic diversity that is important to adaptive evolution. There is a challenge to develop simple inexpensive means to monitor genetic diversity of species on a global scale. Many of the most important practical challenges concern application of current genetic knowledge to the management of threatened species.