Phragmites australis (Cav.) Trin. ex Steud. is virtually cosmopolitan and shows substantial variation in euploidy level and morphology. The aim of this study was to assess clone-specific differences in morphological, anatomical, physiological and biochemical traits of P. australis as affected by the geographic origin, the euploidy level (4 x, 6 x, 8 x and 12 x), and to assess differences between native and introduced clones in North America. Growth, morphology, photosynthetic characteristics, photosynthetic pigments and enzymes were measured on 11 geographically distinct clones propagated in a common environment in Denmark. Any differences between the measured parameters were caused by genetic differences between clones. Overall, the largest differences between clones were found in ontogeny, shoot morphology and leaf anatomy. The North Swedish clone was adapted to short growing seasons and sprouted very early in the spring but senesced early in July. In contrast, clones from southern regions were adapted to warmer and longer growing seasons and failed to complete the whole growth-cycle in Denmark. Some clones from oceanic habitats with climatic conditions that do not differ much from conditions at the Danish growth site did flower in the common environment. The octoploid genotype in general had larger dimensions of leaves, taller and thicker shoots and larger cell sizes than did the hexaploid and tetraploid clones. The dodecaploid clone was neither bigger than the octoploid, nor significantly different from tetraploid and hexaploid clones in most of the morphological characters observed. Stomatal density decreased with increasing ploidy level, while length of guard cells increased. Tetraploid clones generally had morphometric dimensions, similar to hexaploids. Hence, polyploidy did not always result in an increase in plant size, probably because the number of cell divisions during development is reduced. Four North American clones were included in the study. The clone from the Atlantic Coast and the supposed invasive European clone resembled each other. The Gulf Coast clone differed from the rest of the clones in having leaf characters resembling Phragmites mauritianus Kunth. Thus, morphological characters are not unmistakable parameters that can be used to discriminate between introduced and native clones. The physiological and biochemical processes also differed between clones, but these processes showed considerable phenotypic plasticity and were therefore very difficult to evaluate conclusively. It is concluded that P. australis is a species with very high genetic variability which is augmented by its cosmopolitan distribution, clonal growth form and the large variation in chromosome numbers. It is therefore not surprising that large genetically determined differences in ontogeny, shoot morphology and leaf anatomy occur between clones.