This study evaluated the effects of ecology (plant community, topography and pedology), as well as of climate, on the composition of essential oils (EOs) from two officinal wild plant species (Lamiales) from Apulia, namely Satureja cuneifolia Ten. and Thymus spinulosus Ten. Few scientific data on their chemical composition are available, due to the fact that the first has a limited distribution range and the second is endemic of southern Italy. Results for both species, never officially used in traditional medicine and/or as spices, showed that the ecological context (from a phytosociological and ecological point of view) may influence their EO composition, and hence, yield chemotypes different from those reported in the literature. S. cuneifolia and Th. spinulosus can be considered good sources of phytochemicals as natural agents in organic agriculture due to the presence of thymol and α-pinene. Overall, the obtained trend for EOs suggests a potential use of both species as food, pharmacy, cosmetics and perfumery. Hence, their cultivation and use represent a positive step to reduce the use of synthetic chemicals and to meet the increasing demand for natural and healthier products.