The Japanese giant salamander (Andrias japonicus) is a near threatened species endemic to western Japan and is strictly protected by law. However, available information regarding the genetic diversity and genetic structure in this species, essential for its effective conservation, has been limited. We developed four microsatellite markers from A. japonicus and characterized these markers for two populations of this species, as well as for some captive Chinese giant salamanders (A. davidianus) of unknown original locality or localities. These markers, showing expected heterozygosities of 0.00–0.50 in the former and 0.63–0.89 in the latter, will be useful in documenting population genetic properties for each of the two species.