Agave durangensis is a wild endemic species of Mexico, which supports a regional mescal industry. The reproduction of A. durangensis is mainly sexual, conferring it a high variability. For the mescal manufacturing, A. durangensis is collected from wild populations, affecting their reproductive success and demographic performance. We evaluated the morphological variation, carbohydrate content, and genetic structure of A. durangensis plants coming from a single mother plant, to identify lines with some agroindustry potential. Three different morphological and genetic groups were distinguished. According to Mantel tests (r = 0.71), statistical correlations between morphological (Mahalanobis distance) and genetic (Fst) distances (r= 0.71), as well as between carbohydrate content similarity matrix and morphological traits (r= 0.477) were found. The high correlation values suggested that the use of genetic markers combined with morphological traits could be useful as a tool for the selection of high carbohydrate production lines to establish cultivars, which would have conservational implications.