The binturong Arctictis binturong is a threatened carnivore (Mammalia) that ranges throughout the forests of South-east Asia. This study evaluates the genetic diversity of captive binturong populations in European zoos and attempts to assess their geographic origin. We sequenced the hypervariable region 1 of the mitochondrial control region of 56 binturongs, among which 20 had a known geographic origin. We showed that at least two distinct geographic clades exist and were able to assess the geographic clade to which captive individuals belong. Moreover, a low genetic diversity was observed among the captive population of European zoos. Although our results are preliminary, zoo managers should consider the evolutionary significant units identified by this study, and which correspond to recognized sub-species, when planning binturong reproduction programs.