Milleporidae are of high ecological and economic importance, as, together with the scleractinian corals, they belong to the main reef builders of tropical coral reefs. Coral reefs face severe threats mainly due to anthropogenic disturbance. Understanding their population structure and dynamics is crucial for any conservation effort. Here we report the first microsatellite loci for the Milleporidae. Eleven polymorphic markers were developed for the hydrozoan corals Millepora dichotoma from the Great Barrier Reef (Australia) and tested for amplification in M. dichotoma from the Red Sea (Egypt), as well as for Millepora platyphylla from the Pacific Ocean (Moorea, French Polynesia). All loci were variable with 4–15 alleles per locus. Nine loci were transferable between geographic regions and species. These are the first microsatellites for hydrozoan corals. They will provide valuable tools for characterizing the population structure and genetic diversity of the group thereby benefitting coral reef conservation.