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In the context of food sovereignty, it is essential to distinguish and give value to national products, especially those from artisanal production. Argentina and Chile mussel production occurs at different scales (artisanal vs industrial), is targeted to different species and is developed in different environmental contexts, but in the market the two products are labelled and offered as the same. We evaluated the use of the shell shape to distinguish between mussels from these two countries and among crops, using Landmark-based geometric morphometrics. We compared individuals from five crops from Argentina and six from Chile to assess their shell shape variations using various multivariate statistical methods. Our results showed significant differences between the average shell shape from each country. While crops from Argentina were different among themselves, the crops from Chile were similar. The misclassification rate, using the shell shape variables, between countries was lower than 3%. We hypothesize that the shell shape variations inside the country reflect the environmental effect on the phenotype. Our results show noticeable differences in the shell shape between South American mussels from Chile and Argentina, proving that the shell shape variation could be used as a biomarker to the designation of origin of the product. [ABSTRACT FROM AUTHOR]