Macrophytes play important roles in shallow aquatic ecosystems. Stable isotope signatures of macrophytes indicate the environmental conditions and macrophyte contributions to food webs. However, macrophyte isotope signatures have been studied less than isotope signatures of other organisms. We determined the stable C and N isotope signatures of 10 aquatic plant species from Poyang Lake wetland (Wucheng, Yongxiu County) and Nanji wetland (Nanjishan, Xinjian County) in Jiangxi Province, which are Chinese national nature reserves, among different seasons. The isotope signatures for different species and seasons were significantly different. The dominant macrophyte species were Potamogeton malaianus and Nymphoides peltatum. The isotope signatures for different organs of these two species were determined. Both δ13C and δ15N values were higher for P. malaianus than for N. peltatum stems, roots and leaves, and δ13C varied less for N. peltatum than for P. malaianus organs. The δ13C and δ15N values for P. malaianus organs increased in the order rootsstems>leaves, and δ15N values for N. peltatum organs increased in the order roots