The Chilean fjord region, situated between 42 and 56 °S, forms one of the most ragged shorelines and belongs to the ecologically and biogeographically least understood marine regions of the world. A labyrinth of fjords, channels, and islands extends over 240,000 km2 and creates a coastline of more than 80,000 km. Due to strong abiotic gradients, numerous habitats are created, which are further diversified by temporal dynamics (tidal cycle, seasonal changes in precipitation, temperature, radiation, etc.). The region is a biodiversity hotspot hosting unique and fragile ecosystems. Among the species living here, several are species forming habitats in the ecosystem. These organisms can reach high densities conforming the so-called marine animal forests. Examples are marine animal forests dominated by cold-water stony corals, gorgonians, hydrocorals, brachiopods, polychaetes, giant barnacles, sponges, and ascidians. Many of these communities have been discov- ered only recently. There is also a singular characteristic in this area: exceptionally low pH levels of the waters of Patagonian fjords provide the opportunity to study calcifying organisms in an environment with pH conditions in the same range as the ones predicted by the IPCC for the world oceans in 2100. Despite the scarce ecological and biogeographical knowledge of this area, it encounters an unparalleled economic development including high-impact industry-scale salmonid farming, ambitious infrastructure and industrialization projects, and increasing extractive activities. Baseline research on the abiotic and biotic environment of the region is needed to reach sustainability in the use of the marine resources. Management plans including the establishment of marine protected areas to preserve benthic diversity and ecosystem services are urgently needed.