The alligator snapping turtle (Macrochelys temminckii) has been proposed as a Threatened species under the US Endangered Species Act and is considered Vulnerable by the International Union for the Conservation of Nature. To provide additional markers for conservation genetic studies, we identified 60 potential microsatellite loci, with 38 being polymorphic in M. temminckii, as well as successful cross-amplification of 12 and 32 polymorphic loci in the Suwannee alligator snapping turtle (M. suwanniensis) and Eastern snapping turtle (Chelydra serpentina), respectively. These loci will be useful in genetic studies associated with informing future management decisions for M. temminckii and the other species of Chelydridae.