Sorghum [Sorghum bicolor (L.) Moench] is an important food crop in Burkina Faso. Farmers grow various sorghum landraces, distinguished by their morphological and phenological characteristics. This study aimed addressing how this varietal diversity is managed by farmers, and how their management shape the genetic structures of local sorghum. Diversity levels in ten local sorghum guinea varieties (25 panicles per variety) collected from different farms in three agro-ecological regions across Burkina Faso were assessed using nine agro-morphological traits and twelve SSR markers. The importance of phenotypic intra-varietal diversity in early, intermediate and late maturing varieties varied in relation to the observed trait. The genetic analysis specified that the highest diversity rates were in the late maturing varieties (3.3 for allelic richness and 0.47 for gene diversity). Factorial Discriminant Analysis on quantitative traits and cluster analysis based on SSR markers showed that early maturing varieties were discriminated from late and intermediate ones, confirming farmers' classification of maturity groups (MG). Multivariate QST and FST values revealed two subgroups of quantitative traits that underwent either stabilizing or divergent selection among MG scale. These results underline the role of farmer practices in phenotypic and genetic evolution of sorghum. This concept should be well considered in sorghum breeding programs.