Centrosema molle Mart. ex Benth. (sin. C. pubescens Benth.) is among the most important tropical legumes used for forage and green cover. With the purpose of studying the genetic variability of a germplasm collection of the species, 34 accessions were evaluated using four AFLP primer combinations. Additionally, the association between the genetic groups derived from the molecular characterization and those produced by eco-geographi- cal origin was analysed based on climate classification. The resulting climatic groups were separated mainly in three altitude ranges: 10-180 m.a.s.l., 90-540 m.a.s.l. and 320-936 m.a.s.l. The four primer combinations produced 164 fragments, of which 57% were polymorphic. No duplicate accessions were present. An analysis of principal components showed the presence of three homogenous groups associated with the eco-geography (in particular the altitude) of the collection site. This may suggest an incipient process of differentiation in the C. molle natural populations due to the geographical isolation produced by some particular habitats.