Recovery methods and techniques for archaeological sampling can yield major differences in abundance and anatomo-taxonomical representation of animals, affecting past social and ecological reconstruction. Despite being a common organic material in archaeological sites, faunal remains typically exhibit differential preservation of species and skeletal elements due to pre-and post-depositional processes. This is particularly true for small-sized animals such as certain species of fish, whose often small and fragile fragments are difficult to recover and identify. Here, we present the results of a comparative analysis between two ichthyoarchaeological assemblages from Caleta Vitor 3 in northern Chile (CV3, 18°45 ′ 09 ′′ S), an Early to Middle Holocene (9.2-7.6 ka cal BP) Chinchorro shell midden site. We compare samples obtained and processed, both in the field and the lab, using different recovery techniques. We developed a data standardisation procedure to compare and evaluate skeletal representation, taxa distribution and variations throughout the stratigraphic sequence. Our results show that mesh screen size affects not only the abundance and density of fish but also species representation. Moreover, the identification of small pelagic fish at CV3 sheds further light upon prehistoric fishing strategies and social organisation during the site's early occupation.