Rice genetic diversity partitioning between farms, varieties and, within-variety diversity, were analysed in two villages of Maritime Guinea with contrasted agroecological conditions. One thousand and two hundred individual plants belonging to 45 accessions collected in eight farms were genotyped using 10 SSR markers. The molecular variance was evenly shared between and within accessions, while the farm effect was almost nil. Local varieties had a multi-line genetic structure. The number of multilocus genotypes was proportional to the utilisation rate of the variety in the village. The F ST values between different accessions of each variety were significant which indicated low genetic consistency in the variety names. This varietal structure could mainly be explained by the migration phenomenon and the high varietal turnover. Compared to allelic diversity, multilocus genotypic diversity seemed to be the most suitable indicator of the quantitative distribution of diversity at different management scales (accession, farm and village). The within- and between-farm F ST values were in the same order of magnitude. The within-farm diversity was not farm-specific but quantitatively high, i.e. up to 50% of the total genotypic diversity of a given village. Given the relative importance of the within-variety diversity, the in situ approach stands out as the most effective solution. As farms do not host specific diversity the in situ approach could be implemented by working with a small number of farms.