Captive colony genetic management is dependent on knowledge of the colony pedigree. In most zoos, records for colonies held prior to the past decade are incomplete or nonexistent. We have used a nested set of molecular techniques to infer genetic relationships in a colony of 15 lion-tailed macaques after twenty years of unmonitored reproduction. The troop was first divided into lines of matrilineal descent using mitochondrial DNA RFLP patterns. Paternity and maternity were then assigned on the basis of DNA fingerprint analysis. As mtDNA is maternally inherited, it is of no use in paternity assessment, but enabled subdivision of the colony into maternal lines. DNA fingerprinting would have been of little use by itself because of high levels of relatedness in several generations of offspring within the colony. The combination of the two techniques, however, enabled strong inference of both paternity and maternity in all cases. These data were instrumental in the inclusion of this troop in the AAZPA Species Survival Plan.