Consumers are increasingly interested in the geographical origin of the foodstuff they consume as an important characteristic of food authenticity and quality. To assure the authenticity of the geographical origin, various methods have been proposed. Stable isotope analysis is a method that has been extensively used for products such as wine, oil, meat, while only a few studies have been conducted for the discrimination of seafood origin and especially for mullet roes or bottarga products. Analysis of the stable isotopes of C, N and S of Bottarga samples from four different origins were carried out. The values of δ15N (5.45‰) and δ34S (4.66‰) for the Greek Bottarga Product named ‘Avgotaracho Messolongiou’, from Messolongi lagoon were lower than other areas while δ13C values were higher (−14.84‰). The first results show that the stable isotopes ratios of carbon, nitrogen and sulphur could be used to discriminate the Greek Protected Designations of Origin Bottarga product ‘Avgotaracho Messolongiou’ from other similar products.