Micromeria presents eight species in Tenerife, and from these, three are endangered or critically endangered. In this paper we use a 454 run from M. hyssopifolia to develop and characterize 16 new microsatellite markers and test them using 19 individuals from two populations of this species. The number of alleles per locus varied from 2 to 10 and observed heterozygosity ranged from 0.125 to 0.900. Most loci successfully amplified in the threatened species M. densiflora, M. glomerata and M. rivas-martinezii and were also polymorphic. These loci will be valuable tools for assessing the genetic diversity of these endangered species.