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Background The green sea urchin Strongylocentrotus droebachiensis has a wide circumpolar distribution and plays a key role in coastal ecosystems worldwide by destructively grazing macroalgae beds and turn them into marine deserts, so-called barren grounds. In the past decades, large established kelp forests have been overgrazed and transformed to such barren grounds on the Norwegian coast. This has important repercussions for the coastal diversity and production, including reproduction of several fish species relying on the kelp forests as nurseries. Genetic diversity is an important parameter for the study and further anticipation of this large scale phenomenon. Findings Microsatellites were developed using a Norwegian S. droebachiensis individual primarily for the study of Northeast Atlantic populations. The 10 new microsatellite loci were amplified using M13 forward tails, enabling the use of M13 fluorescent tagged primers for multiplex reading. Among these loci, 2 acted polysomic and should therefore not be considered useful for population genetic analysis. We screened 96 individuals sampled from 4 different sites along the Norwegian coast which have shown unexpected diversity. Conclusions The new microsatellite loci should be a useful resource for further research into connectivity among S. droebachiensis populations, and assessing the risks for spreading and new overgrazing events.