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The fan mussel, <i>Pinna nobilis</i>, represents the largest bivalve endemic to the Mediterranean Sea. Since 2016, dramatic mass mortality of this species has been observed in several areas. The first surveys suggested that <i>Haplosporidium pinnae</i> (currently considered species-specific) was the main etiological agent, but recent studies have indicated that a multifactorial disease may be responsible for this phenomenon. In this study, we performed molecular diagnostic analyses on <i>P. nobilis</i>, <i>P. rudis</i>, and bivalve heterologous host species from the island of Sardinia to shed further light on the pathogens involved in the mass mortality. The results support the occurrence of a multifactorial disease and that <i>Mycobacterium</i> spp. and <i>H. pinnae</i> are not necessarily associated with the illness. Indeed, our analyses revealed that <i>H. pinnae</i> is not species-specific for <i>P. nobilis</i>, as it was present in other bivalves at least three years before the mass mortality began, and species of <i>Mycobacterium</i> were also found in healthy individuals of <i>P. nobilis</i> and <i>P. rudis</i>. We also detected the species <i>Rhodococcus erythropolis</i>, representing the first report in fan mussels of a bacterium other than <i>Mycobacterium</i> spp. and <i>Vibrio</i> spp. These results depict a complicated scenario, further demonstrating how the <i>P. nobilis</i> mass mortality event is far from being fully understood.