The Atacama Desert coast (18–30° S) presents one of the earliest chronologies in the South America region, whose first occupations date from ~ 13,000 cal BP. Since that time, coastal and marine resources have been a common component at sites along the littoral zone. Fish species have been particularly important, as have the fishing technologies developed and used by the coastal communities. However, even though several archaeological sites have been studied, there is no systematic macro-regional analysis of early fisheries along the Atacama Desert coast. Furthermore, differences in theoretical and methodological approaches, as well as research objectives, hinder comparisons between ichthyoarchaeological assemblages. Here, we present a comparative analysis of the Atacama Desert fish data obtained from publications and gray literature from ten archaeological sites dating from the Terminal Pleistocene to the Early Holocene. Through the standardization of contextual and ichthyoarchaeological information, we compared data using NISP, MNI, and weight to calculate fish density, richness, and ubiquity, in order to identify similarities and differences between assemblages. This exploratory approach aims to contribute to studies of fish consumption in the area, as well as proposing new methodological questions and solutions regarding data heterogeneity in archaeozoology.