The genetic status of the critically endangered Mississippi sandhill crane (Grus canadensis pulla) was analyzed using 2009 studbook data from the U.S. Fish and Wildlife Service managed captive breeding and release program. Microsatellite DNA data provided information on shared founder genotypes, allowing for refined analysis of genetic variation in the population, and informed breeding recommendations. The genetic variation observed in the Mississippi sandhill crane was contrasted with variation observed in the Florida sandhill crane (Grus canadensis pratensis). Results show far less variation in the Mississippi population. Results also suggest that while gene flow no longer occurs between the two populations, the introduction of cranes from the Florida population would help to increase the observed genetic diversity of the Mississippi sandhill crane population.