The present study shows the pharmacognostic and phytochemical studies on the flowers of Cordia sebestena L. belongs to the family Boraginaceae. C. sebestena L. is found primarily in tropical and subtropical regions of the American, Asian and African continents. Though it is an important plant, until date no pharmacognostic work is found on its parts such as flowers. Various organoleptic characters were recorded by macroscopic study. Microscopic study of the flowers were also conducted which shows the presence of fibers, calcium oxalate crystals and multiple types of trichomes, along with fluorescence analysis. The present study also deals with the Fourier transform infrared spectroscopic analysis of C. sebestena L. FT-IR spectra revealed the presence of C-H, C=C, C-N, C-O and aromatic groups. Chemical composition of the hexane extract of the flowers of C. sebestena L. was detected through GC-MS and spectrum achieved through GC-MS were correlated with the database of National Institute of Standards and Technology (NIST) which comprise of beyond 62000 outlines of the mass spectrum. GC-MS analysis of n-hexane extract shown the existence of Retinoic acid, lupeol, β-sitosterol, stigmasterol, hexadecanoic acid along with fatty acids, esters, alkaloids and alcohols. These pharmacognostic and phytochemical studies can be valuable towards giving reliable proof of the quality of the plant which can benefit health professionals and herbal medicine manufacturers.