The giant water bug (Abedus herberti) is a large flightless insect that is a keystone predator in aridland aquatic habitats. Extended droughts, possibly due to climate change and groundwater pumping, are causing once-perennial aquatic habitats to dry, resulting in serious conservation concern for some populations. A. herberti also exhibits exclusive male parental care, which has made it a model organism for studying mating systems evolution. Here we describe 17 novel polymorphic microsatellite loci developed for A. herberti. Number of alleles per locus ranged from 2 to 15, and average observed and expected heterozygosities were 0.579 and 0.697, respectively. These loci can successfully resolve both population genetic structure among sites separated by 3–100 km (F ST = 0.08–0.21, P < 0.0001), and divergent mating strategies within local populations, making them highly useful for conservation genetics studies of this vulnerable species.