Water-tolerant legumes provide bacteria with special ways of invading roots to establish N(2)-fixing symbiosis upon flooding. On well-aerated roots, root hair curling (RHC) invasion is used, whereas, under hydroponic conditions, rhizobia enter the cortex through cracks at lateral root bases (LRBs). Here, we compare the physiological and anatomical traits of these invasions. During waterlogging, accumulating ethylene inhibits the epidermal stages of RHC invasion. LRB invasion circumvents this step by direct colonization of the cortical tissue. By avoiding the epidermis for bacterial entry under hydroponic conditions, the stringent nodulation (Nod) factor perception systems that are active within the epidermis are not needed. Consequently, LRB invasion might be useful for analysing the requirement for Nod factor perception and other signal transduction systems downstream of the epidermis.