Knowledge on the role of climatic and edaphic factors that influence the essential oil production in aromatic plants is essential for the development of strategies for management and conservation. Mexican oregano is a non-timber forest product traditionally harvested from wild populations by the rural Mayan communities. Despite its economic importance, studies designed to evaluate the variation in essential oil production, and its relationship with environmental conditions, are scarce. The main goal of this study was to assess spatial variation in essential oil yield of 14 wild populations located in a bioclimatic gradient in south-eastern Mexico, and explore if such variation was associated with different climatic and edaphic conditions. A multiple linear regression analysis was used to assess the relationship between essential oil yield and climatic and edaphic variables. Geographic variation in essential oil yield was observed among bioclimatic regions, among populations within regions and among plants within populations. Populations located in regions of higher aridity presented higher essential oil yield. Additionally, our results suggested that plants in populations with lower soil water availability, higher nitrogen and iron contents and higher pH values presented higher ssential oil yield. Finally, this study allowed us the identification of high yield germplasm with potential for commercial exploitation.