Genetic diversity in the genus Elaeis was evaluated by the restriction fragment length polymorphism (RFLP) and amplified fragment length polymorphism (AFLP TM) techniques, on a set of accessions from E. oleifera (241 accessions), E. guineensis (39 accessions), and Barcella odora (three accessions), representing the geographical areas of distribution for the genus. RFLPs were detected by hybridizing 13 nuclear and four mitochondrial probes onto blots of total DNA extracted from individuals and digested by one of the following restriction enzymes: EcoRI, BglII, SstI, or EcoRV. AFLP was performed on a subset of the same individuals using only one primer combination. Factorial analysis of correspondences and cluster analysis of the polymorphic fragments, scored as dominant markers, revealed, independently for the nuclear and the cytoplasmic markers, a striking specific and geographical structuring. Moreover, an interesting feature is that the AFLP gave the same results as the nuclear RFLP in terms of genetic diversity analysis. This study reveals a strong structuring inside E. oleifera, according to the geographical origin, and also a slight intraregional structure within the Brazilian-Amazonian origins of the material studied.