Artisanal fishing may be directed at a diversity of target species. Understanding the factors that influencing the choice of fishing resources for sale or consumption helps us comprehend the pattern of use of natural resources and the pressures on the species caught. The commercial value of the species fished influences the fishing effort. Still, other attributes may interfere with the choice of species to be sold or consumed, such as biomass, trophic level, species habitat, and individual preferences. In this paper Dannieli Firme Herbst contributed to the analysis of the variables that interfere with the choice of fishing resources for consumption or sale (commercial value, trophic level, and habitat) among artisanal fishers in a subtropical estuarine system. The team also explored the relationship between the commercial value and the species’ trophic level. They conducted 80 interviews with artisanal fishers from five municipalities around Babitonga Bay, located on the southern coast of Brazil, who fish both invertebrates (crustaceans and mollusks) and fish. They found an overlap between the number of species sold (92) and consumed (79). Fishing resources with higher commercial value, and trophic level tend to be sold, while species with low commercial value, and trophic level are the most consumed by fishers. Furthermore, some species used for consumption and sale are classified with different degrees of threat regarding their conservation status as Critically Endangered (CR), Endangered (EN), and Vulnerable (VU), both at local and international assessments. The results suggest future directions to support sustainable fisheries management in Babitonga Bay based on these data.