South America stands as the last continent to be permanently occupied by humans, although the exact timing and number of initial migrations continue to be subjects of debate. On the basis of current archaeological and genetic evidence, the Americas were inhabited by anatomically modern humans between approximately 25,000 and 15,000 years ago. From 13,000 years ago, groups of hunter-gatherers dispersed into what is now known as Brazil. They used river systems to explore uncharted territories within a few millennia and set the stage for the remarkable cultural, demographic and socioeconomic diversity seen throughout the Holocene era. Some groups relied heavily on marine resources once they reached the coast, where they raised massive shell mounds (locally known as sambaquis). Dating from 7,000 to 1,000 years ago and found along most of the southern Brazilian coast, these mounds contained massive quantities of animal remains and even human burials, which makes them some of the largest pre-Columbian cemeteries in South America. Their decline remains a topic of contentious debate and, as is the case with most ancient populations in Brazil, little is known about the genetic history of the groups who constructed and used them (referred to as ‘Sambaqui peoples’) or about their connection with early and later populations. Ferraz et al., writing in Nature Ecology & Evolution contribute to bridging this knowledge gap by providing ancient population genetic insights in a vast geographical area of South America. The authors report new genome-wide ancient DNA data for 34 humans and reanalyse a further 13 previously studied individuals, spanning 15 archaeological sites from the past 10,000 years.