Chondroitin sulphate (CS) as a major component of the extracellular matrix of numerous connective tissues is responsible for biomechanical properties such as resistance and elasticity. It occurs in different isomeric forms with different sites and degrees of sulfation. The characterization of crude CS and quantitative isomeric identification by high‐performance liquid chromatography (HPLC) requires specific enzymes, expensive reagents, and a complicated analytical process. Poor reproducibility and imprecise quantification were found with other methodologies. Raman spectroscopy allows rapid and reproducible identification of CS isomers offering specificity and avoids the need for sample pretreatment or external markers. In the present work, a quantitative identification of major contribution of isomeric chondroitin 4 and 6‐sulphate in crude CS by Raman spectroscopy has been performed. Two quantitative indices have been proposed based on areas of specific bands of interest related to main skeletal modes, an aromatic ring with axial orientation in the case of the major contribution of 4‐sulphate and C‐O‐(S) vibration, which is heavily detected in the case of the major contribution of 6‐sulphate. Both mammalian and fish sources of CS were used to validate the ability of mentioned indices to discriminate between prevalence of 4‐sulphate, 6‐sulphate, or none of them. Correspondence of given results with HPLC was demonstrated.