Coastal habitats worldwide are threatened by invasive alien species (IAS) that can alter community and ecosystem processes. Invasions are of particular concern for the Mediterranean Sea, and IAS-related descriptors of good ecological status have been recently proposed in European reference regulations. Here, the occurrence of the Atlantic blue crab Callinectes sapidus was analysed in two Mediterranean coastal habitats, the Acquatina lagoon and Torre Colimena basin (SE Italy). The blue crab is to date recognized as an IAS; however, quantitative information on abundance patterns of the species are scant, and its functional role in European waters is virtually unexplored. Blue crabs were sampled seasonally using crab traps. Specimens were enumerated, sexed, and measured. In addition, in both habitats the carbon and nitrogen isotopic signatures of C. sapidus were determined at its maximum seasonal abundance, and compared against those of other representatives of the benthic food web. In the Acquatina lagoon, C. sapidus was collected only in spring and summer, while other autochthonous crab species were predominantly captured in winter and autumn. In contrast, in the Torre Colimena basin the blue crab was the only captured brachyuran; it was collected during the whole sampling period, and showed summer abundances more than twice as higher than those observed in the Acquatina lagoon. In both environments, juveniles and ovigerous females were sampled, and males dominated over females. Condition factors calculated using individual width-weight data showed that blue crabs from the Torre Colimena basin had higher condition factors compared to those from the Acquatina lagoon. Independently from the environment, Callinectes sapidus d13C values in summer were consistent with those characterizing autochthonous crabs and other representatives of the macrozoobenthos. Its d15N signature, however, varied significantly, suggesting that in the Acquatina lagoon the species may have more predatory trophic habits. Our study indicates the occurrence of established populations of Callinectes sapidus in both study sites, yet characterized by different biological characteristics and roles within the local benthic food web. The results are compared to information on blue crab populations in their native habitats, while their ecological implications are discussed in the context of the effort currently made to clarify the concomitant effects of invasions and climate change on marine ecosystems.