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Knowing the distribution and eco-geography of native Onobrychis altissima and O. cyri in Azerbaijan is critical for the implementation of strategies for their conservation and sustainable use. This study includes 27 specimens from nine wild populations of O. altissima and O. cyri collected from their natural habitats in Azerbaijan. The aims of this study are to provide a detailed morphological and eco-geographic characterization of O. altissima and O. cyri, to determine the distribution and environmental variables that define the eco-geographic zones native to Azerbaijan, and also to determine the priority areas for in situ conservation of native Onobrychis germplasm in Azerbaijan. Besides, research work was carried out for the purpose of clarifying the distribution areas, discovering more resistant species for selection, as well as enriching the genetic resources and Her-barium Fund. The specimens were biometrically assessed using 34 quantitative and 10 qualitative morphological characters. At each site, we recorded eco-geographic data regarding longitude, latitude, altitude, slope inclination, slope orientation, maximum and minimum temperatures, annual precipitation, relief, as well as soil traits including texture, humus, organic carbon, total nitrogen, pH, phosphorus pentoxide, potassium oxide, and magnesium. Cluster analysis of morphological characters showed that the nine populations could be divided into three main groups. Furthermore, principal component analysis (PCA) of eco-geographic data is discussed. The article presents tables and phenograms reflecting some eco-geographic information and a distribution map of the species.