Rice is one of the most important crops in the world and is the first whose genome was completely sequenced. This landmark accomplishment placed O. sativa as a leading model in plant biology, especially for cereals. The genus Oryza includes 23 species, two of them independently domesticated in Asia and Africa. Wild species of Oryza contain a reservoir of useful agronomical traits which could be exploited for the benefit of rice agriculture, which is facing global problems as other crops, mainly due to a rampant increase in the human population and progressive deterioration of soils and water supplies. The Oryza Mapping Alignment Project has opened great opportunities to tap the genetic potential encapsulated in these species. Four BAC libraries generated from the African species of Oryza: O. barthii, O. glaberrima (AA genome), O. punctata (BB genome) and O. brachyantha (FF genome) were fully characterized and shown to provide enough coverage to represent their respective genomes. BAC clones from these libraries were fingerprinted and end-sequenced to assemble physical maps that were heavily manually edited using the sequence of O. sativa as a reference genome. The physical maps showed high coverage for all the species across all chromosomes. Both, BAC libraries and physical maps were used to investigate synteny and structural variation. The four species show high colinearity to the reference genome, although synteny perturbations were detected, including contractions, expansions, and putative inversions and translocations, which potential have an important impact in the evolution of these species.