• Premise of the study: Microsatellite primers were developed for the first time in the genus Filago (Gnaphalieae: Asteraceae). These markers will facilitate low-scale phylogenetic, phylogeographic and population genetics studies within the genus Filago. • Methods and Results: Nine pairs of microsatellite primers were identified and optimized on two species of Filago using a microsatellite-enrichment library method and 454 GS-FLX technique. The set of primers amplified tri- to hexanucleotide repeats, and showed one to six alleles per locus for both species: F. gaditana and F. carpetana. Transferability was performed in 29 samples corresponding to nine representative species of Filago. • Conclusions: The results indicate the utility of the newly developed markers, which will be useful to go deeper into the phylogenetic relationships among the taxa within Filago. These microsatellites will enable phylogeographic, reproductive and genetic variation studies.