Helichrysum italicum (Roth) G. Don is an important medicinal plant native to the Mediterranean region. Positive effects of the biological compounds on human health have been demonstrated by in vitro and in vivo studies. However, most studies so far have focussed mainly on the chemical composition of the essential oil, while the importance of the genotype has been neglected due to the lack of effective molecular markers. The latter is particularly important due to the complex taxonomic classification (the existence of subspecies and interspecies hybrids poses a challenge for the classification of species and subspecies) and cross-pollination, which contributes to high genetic and phenotypic diversity within populations. The aim of our study was to initiate genomic studies and develop SSR markers to identify genotypes. Initially, genomic DNA was sequenced using Ion Torrent technology, utilising a shotgun approach. The assembled contigs of the nuclear genome and chloroplast genome¹ were used to develop 24 highly informative nuclear microsatellite markers² and 16 chloroplast microsatellite markers³. Considering that H. italicum is in the early stages of domestication and cultivation in the agroecosystem is usually based on unverified plant material, the newly developed molecular markers represent a valuable tool for the identification of genotypes with different chemical compositions. Microsatellites are also useful in plant breeding for the control of parentage, for the authentication and traceability of plant material on the market, for the protection of local products and geographical origin, and for the exploration of genetic resources in botanical studies. Due to their transferability, they are also useful for research on related species. This paper presents the benefits and applicability of microsatellites and the results of recent genetic research on the immortelle.