Variation in ploidy levels in Phragmites australis is a well-documented phenomenon although North American populations are less studied than European ones. It has been suggested, based on morphological measurements, that native and introduced P. australis subspecies in North America represent different ploidy levels. The objectives of this study were to assess whether guard cell size and stomatal density, morphological differences indicative of variation in ploidy level between native and introduced P. australis, are truly associated with different ploidy levels as measured by flow cytometry. Significant differences in guard cell size and stomatal densities were found between subspecies, with native plants having larger guard cells and lower stomatal density. However, no differences in 2C DNA content were found. Although these morphological measurements are significantly correlated with subspecies and can be added to the list of useful morphological characters distinguishing the two subspecies, it does not appear that they are accurate indicators of ploidy levels. Potential implications of these differences on the invasion biology of introduced P. australis are discussed.