Reed canarygrass (Phalaris arundinacea L.) is a cool-season perennial grass widely distributed throughout North America, Europe and Asia. P. arundinacea is currently considered a major invasive plant species in the USA. Despite recent concerns that P. arundinacea has become an invasive plant species in Japan, differences between invasive and native Japanese genotypes remain unclear. We used flow cytometry to clarify genome size differences among 14 populations of putative native Japanese P. arundinacea genotypes and three exotic cultivars. The average genome size of the 14 Japanese populations and the three exotic P. arundinacea differed significantly (P < 0.05) and ranged from 4963.90 to 5166.69 Mbp/C. These results implied that the sampled populations included native Japanese genotypes. These populations may be useful in discriminating between invasive and native Japanese P. arundinacea genotypes.