The genus Phragmites includes taxa that are very difficult to distinguish macroscopically, and even genetically. To better discriminate these taxa, microscopic traits, such as the epidermis of floral bracts and leaves, and leaf anatomy, were investigated. In the Old World, four distinct giant reeds species (> 3 m) were delineated: two tropical species, P. karka and P. mauritianus, and two Mediterranean species, P. altissimus and P. frutescens. Previously included within P. australis sensu lato, the rehabilitation of P. altissimus and P. frutescens is supported by relevant distinctive characteristics. Conversely, the small reeds (< 3 m) from temperate to cold regions form a distinct group. Although this group is still difficult to subdivide with epidermis traits, three taxa can be separated using leaf anatomy: both the Afro-European and the Australian-E. Asian P. australis sensu stricto, and P. japonicus. Using iodine green solution, we link our morphological analyses with previous genetic clustering, the green coloration of floral bracts and margin leaf teeth matches with the presence of nuclear waxy gene bands in P. frutescens and P. mauritianus (100 bp), and P. altissimus (200 bp), while P. karka, P. australis subsp. australis and P. japonicus have no coloration nor waxy band. While leaf anatomy features seem to be correlated with eco-climatic conditions, the epidermal traits delimited other clades. For leaf epidermis P. karka, P. mauritianus, and P. frutescens present the more ancestral characters, whereas P. australis, P. japonicus, and P. altissimus possess derived traits. Lastly, floral bract epidermis traits separate two divergent evolutionary lineages from the basal P. karka.