Morphological and chemical characterization of phytoliths from aerial and underground parts of Arundo donax L. and Phragmites karka (Retz.) Trin. ex Steud. was undertaken to substantiate their taxonomic demarcation with reference to one representative species of each genus. Thirty phytolith morphotypes including some new ones were recovered. Apart from individual types, diagnostic phytolith assemblages unique to Arundo donax L. included long trapezoids, narrow bilobates, orbicular, polylobate, spiral and rugose elongate morphotypes. Phragmites karka (Retz.) Trin. ex Steud. was marked by an assemblage of polyhedral, tracheid, cylindric, cross, dendritic, quadrilobate and the rondel morphotypes. Morphometric data for shape descriptors were analysed by descriptive statistics and t-test (for independent-samples) using Paleontological Statistics (PAST) software. Estimation of total silica content revealed higher values for Phragmites karka (Retz.) Trin. ex Steud. than Arundo donax L. from most of the parts. Elemental analysis of phytolith morphotypes from various parts in both the species revealed the presence of Aluminium (Al), Calcium (Ca), Chlorine (Cl), Copper (Cu), Iron (Fe), Magnesium (Mg), Nitrogen (N), Potassium (K) and Titanium (Ti) in small amounts in addition to major elements including Carbon (C) and Oxygen (O) and Si (Silicon). Principal Component Analysis (PCA) of elemental composition grouped Arundo donax L. (leaf) and Phragmites karka (Retz.) Trin. ex Steud. (leaf) together in a single group. The Si (wt%) amounts varied significantly among various parts of Arundo donax L. (p≤0.05), whereas differences with Phragmites karka (Retz.) Trin. ex Steud. parts were insignificant. Similarly, Si (wt%) between the various parts of both species showed significant differences (p≤0.05). Chemical characterization of silica from leaf and synflorescence of both the species using X-ray Diffraction (XRD) showed polymorphic forms of silica and zeolites. Fourier Transform-Infrared (FTIR) Spectroscopy has confirmed the presence of silanol group and siloxane linkages in all the samples.