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The Atlantic blue crab Callinectes sapidus Rathbun, 1896 is native in the western Atlantic, however it is a non-indigenous species across Europe since 1900, among other world regions. In this paper, we report the first occurrences of this species in the Ria Formosa lagoon and in the Guadiana estuary (SW-Iberian Peninsula, Europe) which occurred in 2016 and July 2017, respectively. We hypothesize that the introduction of this species into these ecosystems might be due to the expansion of the Guadalquivir estuary population through natural processes (larval advection, active movement), or due to unintended introduction events after being transported aboard fishing boats, or, less likely, through ballast water. Changes in Guadiana’s river flow after the construction of the Alqueva dam might also explain the presence of another non-indigenous species in the Guadiana estuary. The hypotheses presented, regarding the introduction of the Atlantic blue crab into these ecosystems and of its co-occurrence with other decapod species, are framed in a broader context to serve as a future research framework. The use of the Atlantic blue crab as a new fishing resource is also proposed, namely if it is to be used exclusively by local communities and if no deleterious impacts upon other fisheries and the ecosystem occur from this new fishery.