In the present work, the rapid identification of elements and their relative chemical composition in various Peganum harmala seed samples were investigated using a calibration-free laser-induced breakdown spectroscopy technique (CF-LIBS). A pulsed Nd:YAG laser-source with a 5 ns pulse-duration, and 10 Hz pulse repetition rates providing 400 and 200 mJ energy at 1064 and 532 nm wavelength, respectively, was focused on the Peganum harmala seed samples for ablation. A LIBS 2000+ spectrometer within the wavelength range (200 to 720 nm), emission-spectra were recorded. The measured spectra of the Peganum harmala sample gives spectral lines of Carbon (C), Magnesium (Mg), Lithium (Li), Sodium (Na), Calcium (Ca), Silicon (Si), Iron (Fe), Strontium (Sr), Copper (Cu), Potassium (K), and Lead (Pb). A CF-LIBS technique has been employed for the compositional study of the elements exist in the Peganum harmala seed samples. The measured results demonstrate that C, Mg, and Ca are found to be major elements in the Peganum harmala seed samples with compositions of ~36.64%, ~24.09%, and ~19.03%, respectively. Along with the major elements, the elements including Li, Na, Si, K, Fe, and Sr were identified as minor elements with compositions of ~2.87%, ~2.33%, ~3.72%, ~7.17%, ~2.83%, and ~1.14%, respectively. Besides Cu (~8.07 μg/g), and Pb (~1.10 μg/g) elements were observed as trace elements exist in the Peganum harmala seed samples. Furthermore, the electron number density including the plasma excitation-temperature were calculated using the stark-broadening line profile method and the Saha–Boltzmann plot method, respectively. The plasma parameters versus laser-irradiance and the distance from the sample were further investigated. Moreover, a principal component analysis (PCA) method was also utilized to the spectral data obtained by using LIBS to discriminate various seed samples with four classes, namely, α, β, γ, and Δ. Three principal-components (PCs) calculated from eigenvalues of score matrix described 87.6%, 4.6%, and 2.5% of total variance for PC1, PC2, and PC3, respectively. The LIBS spectral data variance covered by the initial 3 PCS was found as ~94.7% of total variance. The PCA results have successfully demonstrated the different classes of the Peganum harmala seed samples based on the different doping compositional ratios of the Zn element. This study confirmed the feasibility and ability of LIBS and PCA for the rapid analysis of Peganum harmala seed samples. Finally, the results achieved using CF-LIBS were incorporated with those obtained from the XRF and EDX analytical techniques.