Continuous-flow isotope ratio mass spectrometry (CF-IRMS) of deuterium, carbon, nitrogen, oxygen and sulfur has been used to analyse samples of pure chondroitin sulfates from known animal sources (shark, squid, salmon, pig and bovine). There is a need to control the origin of this dietary supplement, which is extracted from several types of animals: for traditional, ethical, or economic reasons, a given source of natural products of animal origin can be preferred to another, and can therefore have a different price. Twenty-three samples collected in Europe and Asia were analysed by IRMS. The results, especially the isotopic deviations of sulphur, oxygen and deuterium, show a significant discrimination between marine and terrestrial origins of this compound which will provide a convenient and efficient way to control the declared sources in the market. The differences observed between origins are further discussed.