The marine ecosystem of the Chilean Patagonia is considered structurally and functionally unique, because it is the transition area between the Antarctic climate and the more temperate Pacific region. However, due to its remoteness, there is little information about Patagonian marine biodiversity, which is a problem in the face of the increasing anthropogenic activity in the area. The aim of this study was to analyze community patterns and environmental characteristics of scavenging crustaceans in the Chilean Patagonian Sea, as a basis for comparison with future situations where these organisms may be affected by anthropogenic activities. These organisms play a key ecological role in marine ecosystems and constitute a main food for fish and dolphins, which are recognized as one of the main tourist attractions in the study area. We sampled two sites (Puerto Cisnes bay and Magdalena sound) at four different bathymetric strata, recording a total of 14 taxa that included 7 Decapoda, 5 Amphipoda, 1 Isopoda and 1 Leptostraca. Taxon richness was low, compared to other areas, but similar to other records in the Patagonian region. The crustacean community presented an evident differentiation between the first stratum (0-50 m) and the deepest area in Magdalena sound, mostly influenced by Pseudorchomene sp. and a marked environmental stratification. This species and Isaeopsis sp. are two new records for science. The discovery of undescribed species evidences that this region needs further studies exploring its biodiversity, which is most likely being already impacted by anthropogenic pressure. The Chilean Patagonian region, located between 41°20′S and 55°58′S of latitude in South America, includes one of the most complex systems of channels and fjords of the planet and holds some of the largest estuarine areas of the world 1. It contains approximately 1,600 km of shoreline and a surface of 2,400 km 2 , being a transition zone of climatological, biogeographical and biological conditions between the Antarctic and the temperate Pacific regions 2. This situation produces an ecosystem that can be considered structurally and functionally unique 3. The ecological and physicochemical characteristics of a fjord are mainly controlled by the interaction of fresh water flowing from the rivers and the entrance of sea water depending on marine currents and tides 4. This creates a strong vertical gradient characterized by a halocline (i.e., a rapid vertical change in salinity), with brackish surface waters and saline intermediate and deep waters. Such marked stratification creates specific environmental conditions that often determine the presence of different species assemblages 5. Within the Chilean Patagonia, the Aysén region is subjected to different anthropogenic activities that have the potential to affect the marine biodiversity.