The bivalve mollusc Pinna nobilis, endemic to the Mediterranean Sea, has been vanishing since 2016 from the whole basin because of an infection by multiple pathogens that caused mass mortality events. In the Eastern Mediterranean, some small populations seem to be resistant to the infection. These individuals could represent the only possibility for the species to recolonize desert habitats. Thus, according to the recommendations of IUCN, looking for living specimens of P. nobilis is a priority. With this goal in mind, we carried out surveys in different areas of Southern Italy, and in 2018, we launched a Citizen Science campaign to involve recreational and professional divers in this challenge. As a result of a monitoring activity carried out in 2022–2024, along the Ionian coast of Apulia, in Southern Italy, we can say that there are no more living specimens there but only empty shells. Concurrent to the vanishing of the queen P. nobilis, its congeneric P. rudis, resistant to the infection, seems to be taking advantage, becoming more common and colonizing habitats once exclusive to P. nobilis. In fact, from different areas of the Mediterranean, sightings of the new possible queen, P. rudis, are increasing, together with the discovery of individuals exhibiting morphological traits that are a mixture of the two species. In some cases, these morphological features are not easy to detect; nevertheless, the presence of these hybrids, resistant to the infection, is important for the conservation of the species.