​The brown macroalga Cystoseira tamariscifolia is a foundation species along the northeastern Atlantic and western Mediterranean Sea. It occurs from lower intertidal rock pools to the shallow subtidal. Anthropogenic pollution and rising seawater temperatures can threaten its local distributions. In order to address impacts of historical and current environmental changes, to quantify effective dispersal and population connectivity, and to provide genetic tools for restoration and coastal management strategies, we have developed ten microsatellite markers, validated on 48 individuals from a single population. With 2–11 alleles per locus, the observed heterozygosity varied between 0.244 and 0.875. All of the developed microsatellites cross-amplified also on Cystoseira amentacea. The ten microsatellite loci developed here show high genetic diversity, making them useful for connectivity and population genetic studies aimed at small to large spatial scales, and provide essential insight for the development of conservation strategies for this important but threatened foundation species.