The Mariana crow (Corvus kubaryi) is an endangered species that is restricted to the islands of Guam and Rota in the Mariana archipelago. Predation by the introduced brown tree snake (Boiga irregularis) has decimated bird populations on Guam, and the crow population there is the last wild remnant of the endemic forest avifauna. The population on Guam is critically endangered and, despite intensive management, the population has continued to decline. Additional management options include intermixing the Guam and Rota populations, but such options are best evaluated within a population genetics framework. We used three types of molecular markers to assay genetic variation in the Mariana crow: mitochondrial DNA (mtDNA) sequences, minisatellites and microsatellites. The two populations could be differentiated by mtDNA sequencing and they differed in allele frequencies at nuclear markers. Thus, the populations could be designated as evolutionarily significant units. However, the Guam population is genetically more diverse than the Rota population, and its survival probability if managed separately is very low. All markers did indicate that the two populations are closely related and separated by a shallow genealogical division. Intermixing the populations is justified by two rationales. First, the apparent population differences may result from recent human activities. Second, a greater amount of genetic information may be preserved by joint management. The translocation of birds from Rota to Guam has begun, but strategies that will ensure maintenance of the variation in the Guam population warrant further exploration.