Understanding the genetic diversity of rice and its population structure is a key to the sustainable in situ and ex situ management of genetic resources. In this study, the molecular analysis of 330rice varieties collected in 59 villages across Burkina Faso was undertaken, using 23microsatellite markers. These markers were found to be polymorphic with an average allele number of 9.4and a mean PIC per locus of 0.58, ranging from 0.034 (RM338) to 0.838(RM1). The 23 SSR markers were powerful enough to separate the two species (O. sativa and O. glaberrima), and to identify a group of most probably resulting from natural crosses between the two species. The glaberrima group were divided into two subgroups in relation with their cultivation ecosystem, deep-water and lowland while O. sativa japonica accessions were clustered in G2. Accessions of O. s.indica species were clustered in three groups (G3, G4 and G5).G3 was composed of accessions of late maturing cropped in lowland environment. G5 accessions were tall and late maturing adapted to deep water condition.G4accessions were of short stature and early maturing adapted to lowland conditions. Using the molecular data and the framework it provided, a core collection of 52 accessions was established that represents the diversity of rice in Burkina Faso. This core collection represents 16% of the collection and account for 89% of the alleles of the whole collection. A core collection of this size could be easily manageable by the national agricultural research institute for conservation in situ or ex situ.