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<i>Melothria pendula</i> L., a wild relative of cucurbit crops, is also used for food and as a medicinal plant in Mexico. The objective of this study was to ecogeographically characterize the known populations of <i>M. pendula</i> in Mexico, determining its adaptive range and possible sites for in situ and ex situ conservation. To achieve this goal, we compiled a dataset of 1270 occurrences of <i>M. pendula</i> from herbarium and botanical databases and individual observations. Adaptive scenarios were generated through the development of an ecogeographic land characterization (ELC) map, preceded by the identification of abiotic variables influencing the species’ distribution. Eleven bioclimatic, edaphic, and geophysical variables were found to be important for the species’ distribution. The ELC map obtained contained 21 ecogeographic categories, with 14 exhibiting the presence of <i>M. pendula.</i> By analyzing ecogeographic representativeness, 111 sites of high interest were selected for the efficient collection of <i>M. pendula</i> in Mexico. Eight high-priority hotspots for future in situ conservation of <i>M. pendula</i> were also identified based on their high ecogeographic diversity, with only three of these hotspots located within protected natural areas. In this study, ecogeographic approaches show their potential utility in conservation prioritization when genetic data are scarce, a very common condition in crop wild relatives.