The giant reed, Arundo donax L. (Poaceae), is a perennial plant species widespread almost all over the world. It is not only considered as an invasive plant, but it also represents one of the most promising energy crops because of its vegetative vigor, high yields, and the low input required for its cultivation. Giant reed reproduces itself only agamically through rhizomes and cane fragments, usually transported by water or through human action. In this work, inflorescences from a collection of clones sampled all over Italy were studied. The results confirmed the sterility of A. donax: no pollen was observed and no seeds were found despite the large size of the inflorescences. Furthermore, 83 clones of the collection were characterized for their inflorescence size and flowering time. We found, for the first time, a significant correlation between the geographical coordinates (latitude) of sampling and the flowering time (r = −0.902 and r = −0.836, respectively at the 4th and at the 5th year after clones transplantation in our experimental farm). A survey of 15 clones, chosen to represent all the Italian territory, was also studied from the genetic point of view using 10 simple sequence repeats molecular markers, to further explore the genetic variability of this species in Italy, and to verify the presence of correlations with the phenotypic differences observed. Although PCA (Principal Component Analysis), AMOVA (Analysis of Molecular Variance), and the calculation of the average pairwise relatedness of populations analysis suggested the presence of three distinct clusters, no correlation was observed between genetic data and inflorescences’ phenotypic data.