The use of single copy nuclear markers is of increasing importance in plant phylogenetics. The generally higher level of variability compared to chloroplast DNA and the ability to use incongruence in a multilocus analysis to determine reticulation patterns makes these kinds of sequence based markers especially useful for species level investigations. However, the prevalence of gene duplication that results from the high frequency of polyploidization events during the evolution of higher plants can impede marker development especially for groups lacking model organisms. Here, we present the strategy and results of marker development for phylogenetic analysis in Micromeria, using publicly available DNA sequences and ESTs from related genera from Lamiaceae, subfamily Nepetoideae. By eliminating markers with signatures of duplication during four steps of marker development, we were able to select 19 primer pairs that resulted in orthologous products for all the species studied. This corresponds to 23% of the initial 84 primer pairs designed. Using an initial sampling of eight individuals, we tested the markers for support of phylogenetic hypotheses related to the evolution of Micromeria on the Canary Islands. While some hypotheses were supported by all markers, an east west split, with a closer relationship between the species of Tenerife and Madeira on one hand and the ones from Gran Canaria and the eastern islands on the other is supported by 12 markers but contradicted by the remaining seven. This indicates that reticulation and inter-island gene flow played a role in the evolution of Micromeria. © 2012 Elsevier Inc.