Abstract Natural pearls have different composition that give them specific properties such as colour, lustre effect and can be classified based on differentiation of various constituents such as crystal phase and the presence of various minerals. The aim of this study was to develop a fast, simple, and non-destructive method for discrimination of the popular Sabah’s pearl that commonly used for bracelet, earring, and necklace. In order to discriminate pearls of different colours, emission spectroscopic method, namely laser-induced breakdown spectroscopy (LIBS) complimented with principal component analysis (PCA) was used. PCA model showed that the first principal component explained 96.44% of the total variance. Calcium, Mercury, and Barium elements mainly deexcited at wavelength 600 to 900 nm attributing to the most effective variables for PC1 while Manganese, and Silicon content were useful in defining PC2. PCA demonstrated clear clustering of pearl samples of different colors. Thus, became a major indicator for successful discrimination of natural pearls of various colors using LIBS spectral data. We can confidently say that this can be made available to use by gems industry for performing a fast quality control of inflowing raw organogenic gems.