Nigella sativa L. seeds oil (NSO) also called as the black seeds oil is popularly known for its uses in a number of disease conditions and several NSO brands are available in the market as the folklore medicine. This study was designed to identify and compare the bioactive constituents present in two different brands of NSO preparations procured from local market. Fourier-Transform Infrared (FT-IR) and Gas Chromatography-Mass Spectrometry (GC-MS) techniques were employed to detect and quantify the constituents followed by chemometric analysis. The phytochemical analyses using GC-MS revealed presence of 40 and 33 constituents, respectively in the two tested oils. Among the major phytoconstituents, Thymoquinone (TQ), alpha-Pinene, p-Cymene, Nerol, Lavandulol, Carvacrol, (Z,Z)-9,12-octadecadienoic acid (Linoleic acid) and Squalene were present in both the samples showing high percent % peak area values. The FT-IR spectroscopic analysis showed presence of characteristic fingerprint functional groups confirming the authenticity of the procured samples. However, there were marked differences in the % area of different constituents making the two oils considerably different from each other. Using chemometric analysis, various dendrograms, heat maps (double dendrograms) and histograms were developed to compare and to make clusters of constituents with similar characteristics that might have originated from the same source.