Casuarina equisetifolia has the widest distribution of all Casuarina species and is a nitrogen-fixing tree planted in tropical/subtropical littoral zones of Asia, the Pacific and Africa for coastal reclamation, charcoal making, pulp and timber. Trichosporium vesiculosum, the causal agent of blister bark disease, is a serious pathogen of C. equisetifolia. The present study was undertaken to understand the molecular mechanisms involved during pathogen cell wall elicitation in this hardy tree species. Transcript profiling during elicitation induced by cell wall components of T. vesiculosum revealed expression of resistance genes; cytochrome oxidase; trans membrane proteins; genes involved in programmed cell death like 26S proteasome and ubiquitin activating enzyme; early nodulin gene, wound inducible metallocarboxy peptidase inhibitor, glucanase, metal binding protein and signal recognition particle. The fold expression of selected transcripts including glucanase, 26 S proteasome, signal recognition particle, cytochrome oxidase and the metal binding protein using RT-qPCR revealed 12-59 fold increase in expression after 48 hours of elicitor treatment. The expression of these transcripts during abiotic stresses like heat, mechanical wounding, salt (NaCl) and drought (PEG) was also analyzed. Glucanase was up-regulated significantly during wounding and heat stress while proteasome was up-regulated 1-4 fold during NaCl, PEG and wounding stress. The novel transcript CeHMA was up-regulated under all the stress conditions. This is the first report on molecular defense in C. equisetifolia and has provided a pool of candidate genes for detailed molecular dissection to further broaden the knowledge on the response of woody perennials during pathogen cell wall elicitation.