Golden-headed lion tamarins (GHLTs), Leontopithecus chrysomelas, are small fruit-eating primates endemic to the Atlantic Rainforest of South-Bahia, and endangered because of the disappearance of their habitat (2006 IUCN Red List of Threatened Species). The Brazilian Atlantic Rainforest has a unique and extremely rich biodiversity, but continuing deforestation has reduced its surface to less than 7% of its original extension (Tabarelli et al. 2005). Several research and conservation projects are currently running in the eld and simultaneously an international captive breeding program has been setup as a backup for the wild population. However, golden-headed lion tamarins were imported from Brazil in small groups. If these consisted of family groups, the current genetic variability in the captive stock might be severely overestimated. Hence we will estimate the genetic relationship between the founders to improve our breeding schemes (e.g. Gautschi et al. 2003). Microsatellite loci make excellent genetic markers for relatedness analyses because they are often highly polymorphic (Blouin et al. 1996). In addition to 14 microsatellite markers, developed for related species and successfully tested for cross-amplication (Galbusera et al. in prep), the authors report here 9 new microsatellite loci that are variable in golden-headed lion tamarins.