Conservation programs benefit from profound knowledge on the species of population of concern. Whereas such information is often absent for threatened species, genetic tools hold several interesting opportunities to recover the data needed to increase conservation success. Within the the Centre for Research and Conservation (CRC), molecular and statistical tools are used to study wild and captive populations and the link between both. Delineating (genetic) differences between populations and species is of prime interest in conservation. Hence, both samples from the wild and musea specimens are analysed (microsatellites, sanger sequencing or NGS) to determine both the taxonomic position (e.g. military macaws, Ara militaris) and to get some glimpse on recent population dynamics (e.g. effect of reintroductions in storks, Ciconia ciconia). In terms of captive breeding, most of this work centres around avoidance of hybridisation. On a “lower” hierarchical level, individual subpopulations are subject of detailed genetic surveys. Often these genetic surveys are tightly linked to one of our in-situ research projects. Genetic analysis on non-invasive stool samples of the elusive Cross river gorilla (Gorilla gorilla diehli) for instance enable us to study for population sizes, social interactions and dispersal rate of this highly elusive and threatened subspecies. These estimates are essential in the modeling (eg. probability of extinction) and management these wild populations. Within ex-situ breeding populations we study the effect of inbreeding depression and the genetic background of several traits (e.g. life-history traits in Congo peafowl, Afropavo congensis and behavioural traits in bonobo’s) and whether genetic diversity (GD) for these traits changes throughout time. The importance of GD within populations is increasingly accepted. Within captive breeding genetic goal are set and evaluated based on pedigrees, which often include gaps (e.g. unknown parentage) and assume founders to be unrelated. Here (genetic) management of breeding programs can be supported by molecular (DNA) analyses. As such, samples of eg. captive golden-headed lion tamarins (GHLT; Leontopithecus chrysomelas) and babirusa (Babyrousa babyrussa) and bonobo’s (Pan paniscus), are currently analysed to resolve questions on founder relatedness and paternity, often by integrating the molecular data with the available pedigree data and samples from the wild. At a the level of the individual, analysing the MHC (Major Histocompatibility Complex) genes of Eurasian black vultures aims to optimize pair formation (and hence breeding & reintroduction success).