This research aims to evaluate adaptation of two contrasting sorghum genotypes to flooding: a landrace from Cameroon described as a “floating sorghum” (Wulaga) and a typical dryland improved variety (Cirad437) from Burkina Faso. Anatomical and morphological features of the basal internodes were quantified in control conditions (drained pots) and long-term flooded conditions from the five-leaf stage for the entire cropping cycle. This study revealed that the Wulaga variety expressed aerenchyma in basal internodes in both control and flooded treatments (constitutive aerenchyma) whereas Cirad437 only developed aerenchyma in flooded conditions (inducible aerenchyma). The level of lignification and epidermis thickness of basal internodes was identical for the two varieties and the two treatments, suggesting that lignin does not contribute to the enhancement of a tight barrier against O2 losses. However, Cirad437 showed shorter and larger internodes in flooded conditions while Wulaga did not show any difference between the two conditions. Results indicate the existence of diversity in adaptive response to flooded conditions for the two varieties. Further studies on phenotypic traits associated with phenology, leaf traits, root traits and yield components, are needed to confirm these preliminary results and to explore a broader range of genetic diversity that could be used for future sorghum breeding programs designed for flood-prone environments.