The successful invasion of alligator weed (Alternanthera philoxeroides) into both aquatic and dry terrestrial environments has been attributed to its phenotypic plasticity and high rates of growth and vegetative propagation. Here, we evaluated whether the anatomical structures of alligator weed make it well adapted to colonize the aquatic-terrestrial transition zone. Anatomical and histochemical analysis revealed an impermeable apoplastic barrier that consists of a cuticle and an endodermis of the adventitious root and stem in both aquatic and terrestrial environment; stem and root possess a periderm in the terrestrial environment; and the root has a lignified cortex and hypodermis in the aquatic environment. A supernumerary cambia produces secondary vascular bundles, parenchyma and adventitious buds. Dilated parenchyma cells exist in the aged terrestrial roots. Aerenchyma tissue and pith cavities in the roots and stems produce air spaces, and the aquatic roots possess large aerenchyma compared with intercellular aerenchyma of terrestrial roots. In summary, phenotypic plasticity of anatomical characters, such as impermeable apoplastic barriers, air spaces, and reproductive supernumerary cambia, may be evidence that alligator weed is well adapted to the aquatic–terrestrial transition zone.