Hazel dormice, Muscardinus avellanarius (Rodentia: Gliridae) are vulnerable to habitat loss and fragmentation, and thus protected by European Directives. We isolated hazel dormouse microsatellite sequences from enriched genomic libraries to facilitate conservation-focussed research, such as population genetics, regarding this threatened species. Fifty-three primer sets were designed from 51 newly isolated loci. Additionally, we redesigned and tested nine primer sets from previously-published hazel dormouse microsatellite sequences. These 62 marker sets were initially tested in eight unrelated individuals. Thirty-nine loci, which were polymorphic and amplified in >88 % of these samples (extracted from hair), were then genotyped and characterised in 22–26 individuals. Of these, 26 autosomal loci (18 new and eight published) adhered to Hardy–Weinberg equilibrium (p ≤ 0.05) and displayed an estimated null allele frequency of <0.10. One loci pair displayed linkage disequilibrium after correction for multiple tests.