In Maritime Guinea, the interpenetration of upland, lowland and mangrove rice growing ecosystems has found expression in the cohabitation of the two rice cultivated species. Recent changes in cropping practices may lead to the replacement of local varieties by modern high-yielding varieties. In the framework build-up of a strategy for the preservation of local varieties, we analysed the extent, the organisation and the specificities of the rice genetic diversity. One hundred seventy accessions collected in farmers' fields were genotyped with 11 SSR markers and phenotyped with 26 morpho-physiologic descriptors. The general organisation of rice genetic diversity in Maritime Guinea, and its tight relationship with the rice growing ecosystems were similar to the one observed elsewhere. The two major subspecies of O sativa-indica and tropical japonic-as well as the two major ecotypes of O. glaberrima-"floating" and "upright"-were present. Moreover, an original genetic compartment was detected, highlighting the occurrence of glaberrima × sativa hybridisation. Allelic diversity was found to be comparable to that noted worldwide for indica and japonica groups of O. sativa, but not as large for O. glaberrima. Given its extent, its original compartment, and its potential for inter-specific and inter-subspecific indica × japonica recombination, the preservation of rice genetic diversity in Maritime Guinea deserves special attention.