Diopatra neapolitana (Delle Chiaje, 1841) is one of the most exploited polychaete species in European waters, particularly in Ria de Aveiro, a coastal lagoon in mainland Portugal, where the overexploitation of this resource has led to a generalized decline of local populations. In an attempt to reduce the impact of harvesting, several management actions were implemented, but, illegal poaching still fuels a parallel economy that threats the sustainable use of this marine resource. The present study evaluated the combination of fatty acid profiles and elemental fingerprints of the whole body and jaws, respectively, of D. neapolitana collected from four harvesting locations within Ria de Aveiro in order to determine if their geographic origin could be correctly assigned post-harvesting. Results showed that both fatty acid profiles and elemental fingerprints differ significantly among locations, discriminating the geographic origin with higher accuracy when combining these two natural barcodes than when employing each individually. The present work can therefore contribute for the implementation of an effective management plan for the sustainable use of this marine resource, making possible to detect if D. neapolitana was sourced from no take zones and if it was collected from the place of origin claimed by live baits traders.