According to recent estimates, the global marine environment has been modified by human activities over almost 90% of the ocean (Jones et al. 2018). Not surprisingly, the deterioration is higher, more evident in coastal areas. Biological and chemical pollution, habitat destruction, over-exploitation, biological invasions and the global threat of climate change and ocean acidification are among the most well documented stressors affecting these areas (Jackson 2008; Rilov 2016; Dailianis et al. 2018).

In the Mediterranean Sea, there is a remarkable coastal marine habitat: submarine caves, the subject of this chapter. Due to its geological history, the Mediterranean coastal margins have an impressive abundance of marine caves (Giakoumi et al. 2013). Many were used by humans during the last sea-level low stand and the fascination they exerted on the archaic mind can be recognized in the wall paintings of one of such caves (eg Collina-Girard 2004). Submerged marine caves are particular environments that are considered refugia or reservoirs of biodiversity in the Mediterranean Sea (Gerovasileiou and Voultsiadou 2012, 2014). Still, the majority has no data on basic aspects such as species composition, structure of communities, function, and response to disturbances (Gerovasileiou et al. 2016, 2017b; SPA/RAC–UN