The southern coast of Santa Catarina is characterized by presenting a dynamic and complex scenario of human occupation, which dates to the 7,500 years BP, displaying several monumental shell mounds which attest that these peoples established a close connection with the lagoon system, which extended to around 1,500 years BP, when there was a change in the appropriation of the landscape. From this period onwards, called the late period, greater variability of sites and a distinct pattern in the construction process are registered, transformations that were chrono-culturally associated with the arrival of the southern Jê groups. With the proposal of understanding the aspects that resulted from this interaction, this research allowed to refine and advance a little more in the knowledge about the relationship between these human groups, the fauna and the paleoenvironment, during the late period of occupation in this region. The zooarchaeological analyzes used in the shell mound Eliza (3,350 cal years BP), in the late sites, Encruzo (1,980 cal years BP), Morro Grande II (1,860 cal years BP), Morro Grande I (1,270 cal years BP), in addition to the associated occupations with the Jê, Campo Bom III (780 cal years BP), Campo II (720 cal years BP), Campo Bom I (650 cal years BP) and Arroio da Cruz I (650 cal years BP), pointed out that these peoples established a very complex interaction with the dynamic coastal landscape, exploring mainly the estuarine-marine environment, whose faunistic recurrence demonstrated an intense capture of fish and bivalves, and to a lesser extent, terrestrial and marine mammals, as well as cartilaginous fish, reptiles and birds. Through the integration of zooarchaeological, chronological and paleoenvironmental data, several aspects were verified that point to a continuity and cultural transformation that occurred from the contact between sambaquieiros and Jês.