The most important structural changes of the marine communities of the Ligurian Sea (Mediterranean Sea) are described and discussed, stemming from scientific contributions published in the last decades. The main causes of disturbance and stress along the coastline were, since long time ago: huge urban, touristic and industrial developments, harbour activities, building of littoral rail- and motorways, beach replenishments, presence of several polluted drainages, impact of fishery activities. Nevertheless, the EQR-CARLIT index recently evidenced a moderate seawater quality and ecological status, indicating a slow, but progressive improvement of the littoral environment. But, in a changing climate, thermal stress anomalies in 1999, 2003 and 2006 determined major changes in the structure of benthic and fish communities. In addition, the plankton showed significant changes, especially in terms of primary production, while the disappearance of some species and the arrival of others, even of commercial interest, were recorded. Starting from the late 1980s, some thermophilous and/or Lessepsian species reached the Ligurian Sea, often determining processes of “meridionalization” and “tropicalization” of the basin. In a relatively short time span, i.e., 30–40 years, the structural complexity of Ligurian marine communities changed dramatically as never observed before in historical times.