The present study assessed the diversity of pheno-morphological and agronomic traits among 31 natural populations of burr medic (Medicago polymorpha L.) from different environments throughout Sicily, and analysed the patterns of phenotypic diversity in relation to the environmental parameters of each collection site. Three commercial cultivars (Cavalier, Santiago, and Anglona) were also included in the study as check cultivars. Two field experiments were performed in 2005–06 in a hilly area of the Sicilian inland. Principal components analysis (PCA) was performed on the sites using geographic, climatic, and pedological data to assess the differences in types of collection sites. PCA was also performed on the accessions using pheno-morphological and agronomic data to establish the importance of different traits in explaining multivariate polymorphisms. Sicilian burr medic populations showed highly significant inter-population differences for all of the recorded pheno-morphological and agronomic traits, and several populations had agronomic attributes that were more pronounced than those of the check cultivars. PCA did not clearly differentiate the accessions according to their habitats of origin, but in some cases, accessions from the same habitat had a tendency to stay together. Populations from drier and warmer habitats flowered earlier and were less productive than those from wetter and colder ones. The large variability in both pheno-morphological and agronomic traits among Sicilian populations may be valuable when searching for suitable M. polymorpha material to exploit in pastures and crop–livestock farming systems in the Mediterranean region.