The black and gold howler monkey (Alouatta caraya) is a neotropical primate that faces the highest capture pressure for illegal trade in Argentina. We evaluate the applicability of genetic assignment tests based on microsatellite genotypic data to accurately assign individuals to their site of origin. The search was conducted on a genetic database to determine the nearest sampled population or to associate them to three clusters described here for the Argentinean populations of A. caraya. We correctly assign 73% of the individuals in the database to nearest population of origin, and 93.3% to their cluster of origin. With this database, we were able to determine the probable origin of 17 confiscated individuals, 12 of which were reintroduced in the province of Misiones and 5 confiscated individuals reintroduced in the province of Santa Fe. Moreover, we also determined the probable origin of 3 individuals found dead in cities in northern Argentina. This approach highlights the relevance of generating genotype indexing databases of species to assist with in-situ and exsitu conservation and management programs. Our results underscore the importance of knowing the origin of individuals for reintroduction and/or species recovery programs and to pinpoint the hotspots of illegal capture of various species.