The heterophyllous macrophyte waterchestnut (Trapa natans L.) produces floating and submerged leaves which are strikingly different in morphology. In the present work, we compared, through cytological, cytochemical and immunocytochemical analyses, the nuclear features of the shoot meristem in floating and submerged buds that produce the different leaves. The occurrence of DNA polymorphism in the two types of leaves was studied by using the random amplified polymorphic DNA (RAPD) approach. The light microscope study of chromatin organization revealed an articulate structure of the nuclei, with prominent chromocentres in both floating and submerged buds. However, the meristematic nuclei of floating buds, as compared to those of submerged buds, displayed peculiar features which seem to be related to a higher proportion of A-T-ricn sequences and a higher level of DNA methylation of the nuclear genome. Moreover, RAPD analysis showed polymorphism between the genomic DNAs of floating and submerged leaves. These results show that organs of an individual plant living in different environmental conditions undergo changes in genome organization which may predispose those organs to function more effectively in different environments.