Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared with its Asian cousin O. sativa. A previous reference genome was published but newer studies highlighted some missing parts. Moreover, global species diversity is known nowadays to be represented by more than one single individual. For that purpose, we sequenced, assembled and annotated de novo three different cultivars from O. glaberrima. After validating our assemblies, we were able to better solve complex regions than the previous assembly and to provide a first insight in pan-genomic divergence between individuals. The three assemblies shown large common regions, but almost 25% of the genome present collinearity breakpoints or are even individual specific.