Abstract Background The bermudagrass (Cynodon dactylon (L.) Pers) roots responded differently in terms of morphological and anatomical characteristics under diverse submergence conditions, and they developed aerenchyma under non-flooding condition. In order to understand these mechanisms, bermudagrass cuttings were used as experimental material to examine their biomass, root morphology, and aerenchyma formation under three different water treatments, including control (CK), shallow submergence (SS), and deep submergence (DS). Results The total root length, root volume, root surface area, and biomass of bermudagrass were largest in CK, followed by SS and DS. However, the average root diameter was greater in each of DS and SS than that in CK. Root aerenchyma formation was observed in CK, and submergence boosted the aerenchyma formation and the root cavity rate. Furthermore, our study found that the process of aerenchyma formation began with the increase of cell volume and cell separation to form a narrow space, and these cells gradually died to form matured aerenchyma cavity, which belongs to schizo-lysigenous aerenchyma. Meanwhile, typical biomarkers of programmed cell death were also observed. Conclusion Overall, these results suggested that submergence inhibited the accumulation of biomass and root growth, but facilitated aerenchyma formation by increasing root diameter.