This study was designed to perform the physicochemical and phytochemical standardization with HPTLC fingerprinting of Nigella sativa seeds in order to establish the standard pharmacognostical parameters of this miracle herb. Different parameters like extractive values; total ash value, acid insoluble ash value and water soluble ash value, moisture content, loss on drying, pH values of Nigella sativa seeds were performed. Preliminary phytochemical screening was done to detect different phytoconstituents by using the Harborne's phytochemical methods. Quantification of phenolic and flavonoid contents, determination of pesticides residues, aflatoxin and heavy metals were also carried out. HPTLC fingerprinting of methanolic extract was performed using CAMAG-HPTLC system connected with win CAT software. Preliminary phytochemical screening of the extracts in different solvent revealed the presence of carbohydrates, phenolic compounds, flavonoids, alkaloids, proteins, saponins, lipids, sterols and tannins. Total flavonoid and phenolic contents in methanolic extract was found to be 1.4 mg/gm and 9.8 mg/gm extract respectively. Concentrations of heavy metals were found within acceptable limits. Pesticides residues and aflatoxins were not detected. The physicochemical and phytochemical standards along with HPTLC fingerprint profile established as an outcome of this research may be utilized as substantial data for identification, purification and standardization of Nigella sativa seeds.