In recent years, mass mortality events of benthic invertebrates have been recorded in the Mediterranean Sea that are related to increased sea water temperatures, as one of the major effects of global climate change. Following a disease outbreak in gorgonians (Eunicella cavolinii and E. singularis) during the summer seasons of 2008 and 2009 in the Gulf of Naples (Tyrrhenian Sea), a gross and microscopic analysis, using both light and electron microscopy (SEM), was conducted. Macroscopically, the dead colonies showed a complete loss of polyps and coenenchyme, exposing their skeletons to settlement by fouling organisms, with other affected colonies exhibiting evident tissue thinning. Histopathology revealed chronic inflammatory lesions at polyps and axial level characterized by amoebocytes infiltration of tissue accompanied by new-apposition of melanin/gorgonin sheets against different kind of pathogens, which were mainly identified as a heterogeneous consortium of filamentous cyanobacteria. This response gradually led to enlargement/hardening of the coral axis, which resembled a wood-like structure at final stage of the disease, and elicited the formation of multiple, inflammatory nodules and capsules, some of which were macroscopically visible. A parallel 16S rRNA and ITS analysis identified Synechococcus, Arthrospira and other uncultured cyanobacteria grouped within Oscillatoriales. Analysis of the temperature in the 10-20 m layer during the sampling period revealed anomalous high temperatures (up to 25°C), particularly in June 2009. These results suggest that a cyanobacterial consortium is involved in the pathogenesis of the inflammatory disease leading to the mortality of Gorgoniaceae in the area. Furthermore, the coral skeleton may serve as a reservoir for the pathogens in cooler seasons. Favourable warmer conditions then lead to pathogen reactivation, resulting in repetitive mortality events.