In vitro propagation methods using ex vitro rooting were developed for Alternanthera philoxeroides using nodal segments procured from mature plants. The explants were surface sterilized with 0.1 % HgCl2 solution and inoculated on semisolid Murashige and Skoog (MS) medium containing various concentrations and combinations of plant growth regulators. All the explants responded, and maximum 8.0 ± 0.4 shoots per node with 4.7 ± 0.7 cm average length were induced from nodal meristems on MS medium supplemented with 2.0 mg/L 6-benzylaminopurine (BAP). The shoots were further multiplied (23.8 ± 1.9 shoots per explant) by repeated subculture of freshly induced shoots on MS medium augmented with 1.0 mg/L each of BAP and Kinetin, 0.1 mg/L indole-3-acetic acid (IAA) and additives. About 85 % shoots were rooted (18.0 ± 0.8 roots per shoot) in vitro on half-strength MS medium fortified with 1.5 mg/L indole-3-butyric acid (IBA). Maximum 96 % shoots were rooted using ex vitro methods, and 7.3 ± 1.0 roots per shoot induced with IBA (300 mg/L). The in vitro as well as ex vitro rooted plantlets were acclimatized successfully in the greenhouse. Biologically significant developmental changes were observed during acclimatization of plantlets, particularly in leaf micromorphology in terms of changes in stomatal frequency and stomatal index. This knowledge helps in understanding the response of the plants toward changed environmental conditions during hardening process. This is the first report on micropropagation of A. philoxeroides using ex vitro rooting method which can be used for the large-scale multiplication of this medicinally important aquatic plant.