In this paper, pod morphological traits of eleven populations of Medicago orbicularis (L.) Bartal., collected from the West, Northwest, and Southwest of Iran, have been assessed. In addition, nuclear ribosomal Internal Transcribed Spacer (nrITS, ITS1+5.8s+ITS2) variation in four populations of M. orbicularis was analyzed. Molecular phylogenetic analysis showed that all accessions of M. orbicularis formed a well-supported monophyletic clade while no geographical patterning was observed.  The result of Principle Components Analysis (PCA) and cluster analysis (Ward’s method) (despite a negative Mantel test), suggested a relationship between the morphology and geographical distribution of the populations.Moreover, three distinctive geographical groups were determined using PCA and cluster analysis. Correlation analyses between ecological variables and morphological traits were often negative. However, altitude, average temperature, and average monthly soil temperature showed positive correlations. Wind's relative effect on all morphological traits has also been observed. Two morphological traits- Seeds Total Number (STN) per pod and Fruit Diameter (FDM)-indicated a significant variation. A direct relationship was observed between the two mentioned characters in all populations.  Paveh (PVH) and Marivan (MRV) with the highest STN and FDM demonstrated useful potential for breeding and conservation programs in the future. Overall, it could be assumed that the high STN in M. orbicularis (comparison with other species of Medicago studied in Iran, such as M. minima, M. sinskiae, and M. polymorpha), as well as the effect of winds on seeds distribution, are two main influential factors in creating geographical pattern and morphological diversity.