The Humboldt Current System (HCS) is one of the most productive marine ecosystems on earth. Humans have inhabited the desert coast of Chile and Peru for the last 12,000 years and have consistently based their subsistence and economy on the marine resources obtained from this rich ecosystem. Archaeological evidence on prehistoric coastal fisheries from the southern coast of the Atacama Desert, shows a Trans-Holocene record on knowledgeable fishers that developed gear to catch species from a wide array of habitats. However, the Holocene was a period with important changes in climate and paleoceanographic conditions that should have played an important role modulating natural conditions of fish habitats. In addition, fishing gear used in the past along the Atacama Desert coast varied through time, providing us clues on changing fishing patterns through the Holocene. Hence, the objective of the study is to examine our understanding of prehistoric fisheries from the area of Taltal (25°S) together with our present knowledge of the environmental factors that modulated it. We present fish data from ten archaeological sites with occupations dated between 12,000 and 1500 cal yrs BP, and discuss patterns of fishing behavior and their relationship to paleoceanographic conditions and fishing gear throughout the Holocene. Our results suggest that fishing strategies used by past communities adapted and took advantage of the dynamics of marine and coastal habitats. Furthermore, Trachurus murphyi, a neritic species and a staple fishery, plays a key role to help us understanding changes in fishing activities throughout the Holocene.