Casuarina junghuhniana is one of the most important members of nitrogen fixing, woody, non leguminous tree in the family of Casuarinaceae. The roots form a symbiotic association with Frankia-an actinomycete that fixes atmospheric nitrogen enabling the tree to tolerate varied environmental constrains. It is a multipurpose tree which is widely used in soil reclamation, agro forestry systems, dune stabilization and in wind breaks. It has also end uses such as pulp wood, fuel wood and as poles for constructions. Increasing work has been reported on genetic improvement and yield of this species, not much work has been documented on the phytochemistry of the tree. Therefore, the present research work focuses on the presence of potent secondary metabolites of Casuarina junghuhniana root. Casuarina junghuhniana root samples were collected from the State Forest Research Institute, Kolappakam, Chennai. Different extracts of root samples were evaluated for the presence of phytochemicals by qualitative and quantitative analysis. Anti fungal activity was tested against different phytopathogens. The maximum zone of inhibition was found against Fusarium oxysporum (20±0.2mm). FT-IR analysis revealed the presence of functional groups such as alkyl halides, aliphatic amines, aromatic amines, nitro compounds, amides, alcohols and phenols. The chromatographic studies such as TLC, HPLC, GC-MS revealed the presence of a rich source of phenols and flavonoids in root extract. The secondary metabolites present in the root may also play an important role in plant growth and resistance to their pathogens and herbivores. Further, this study may also help us to understand the compatibility of Casuarina sp cultivation with different intercrops and to design and promote the suitable intercropping system in agro forestry.