The genera Strobilanthes Blume have a rich history in therapeutic culture all over the world. Asian countries like India, China, Myanmar and Thailand still use Strobilanthes genus-based medicinal preparations for various diseases. Strobilanthes jomyi is a newly discovered species from Kerala, India. Some tribal communities of Kasaragod district still use S. jomyi leaf extract as a wound healing medication. The current study aims to investigate the pharmacognostic, phytochemical and GC-MS analysis of the leaves, stems and roots of S. jomyi. The microscopic, macroscopic, organoleptic, fluorescent, phytochemicals and GC-MS analysis of the leaves, stem, and root of S. jomyi were estimated using various standard protocols. The macroscopic and microscopic characters of leaves revealed the presence of non-glandular trichomes with paracytic stomata in the leaves. The transverse section of the stem and petiole showed the presence of raphides and the root showed the presence of tannin cells. Cystoliths were observed only in the petiole. Powder morphology of leaves, stems and roots revealed the presence of fibers, trichomes, palisade cells, spiral xylem vessels, bordered pit vessels and raphides. The vegetative part of S. jomyi powder exhibited various fluorescent coloration based on numerous chemical treatments along with different tastes, smells, colors and textures by organoleptic assays. Qualitative phytochemical analysis of different vegetative parts revealed the presence of flavonoids and other phytochemicals. GC-MS study revealed that lupeol a significant bioactive compound was present in all the vegetative parts of S. jomyi. The results acquired from this study can be used for the standardization, identification, quality and purity check of plant samples.