Perna perna mussel is a coastal benthic filter-feeder widely cultivated in mytiliculture farms and serves as a resource for local communities engaged in its harvest along the Brazilian coast. This study presents the isotopic ratios (δ13C and δ15N) in the soft tissues of adult mussels from six natural populations in Rio de Janeiro State, southeast Brazil, to evaluate whether they are sensitive enough to distinguish the origin of specimens. The COVID-19 pandemic served as temporal reference, as the quality of coastal waters was influenced by the restrictions imposed during the pandemic. The mean values of δ13C and δ15N ranged from −19.5‰ to −17.3‰, and 6.2‰ to 10.5‰, respectively. The spatial variation of δ13C-δ15N data in the analysed mussels was greater than the temporal variation. The k-means clustering method correctly identified 80% of populations during the pre-pandemic period, 67% in the pandemic, and 50% in the post-pandemic. In most samples, the spatial variation of δ15N (tracer of food source variability) was the primary variable distinguishing the groups of mussels. The isotopic ratios did not reveal a clear trend when using the COVID-19 pandemic as temporal reference. Consequently, the positive environmental changes brought about by the suspension or reduction of anthropogenic activities in coastal waters during the pandemic had minimal impact on the isotopic ratios of mussels at most sampling sites. The utilisation of δ13C-δ15N data to trace the origin of P. perna mussel from natural banks was only partially effective in distinguishing the origin of natural populations across the studied area.
