Micromeria fruticosa is an important crop, is widely used in the Mediterranean basin as food and in folk medicine, owing to its health-promoting properties, partially due to the secondary metabolite composition. However, complete information on the phyto-metabolites in M. fruticosa is still lacking. Plant leaves were extracted in methanol (80%), then the phyto-metabolites were separated on C18 column and an extensive characterization using UHPLC–DAD-ESI–QTOF–MS2 method in two ionization modes was established. A total of 215 phenolics and other compounds were tentatively identified, offering the first comprehensive study available on the phytochemicals from M. fruticosa. Over 180 phytochemicals (87 flavonoids, 41 phenolic acids, 16 terpenoids, 8 sulfate derivatives, 7 iridoids, and others) are reported in Micromeria for the first time. M. fruticosa can be a promising source of functional ingredients and has use in the food, pharma and nutraceutical industries. © 2018 Elsevier Ltd