Sambaquis or shellmounds are archeological sites constructed by hunter-fisher-gatherers that inhabited the Brazilian coast about 10,000–2000 yrs BP. Jabuticabeira II (JABII: 2890 ± 55 to 1805 ± 65 BP) is one of dozens of contemporaneous sambaquis of the Santa Catarina state, South Brazil, and contains hundreds of neatly organized burials, indicating great population density. In order to gather information about the health, diet and way of life of people in JABII, a paleoparasitological, paleogenetic, and micro-human remains investigation was carried out. Pelvic region and environmental control samples from six individuals exhumed from JABII were submitted to microscopic and ancient DNA (aDNA) investigation. Paleoparasitological analyses based on light microscopy were negative. However, a variety of informative microremains were found. Diatoms, fish scales, and algae characterize the marine and estuarine environment. Ipomoea batatas and Zea mays starch grains suggested cultivated items as part of their diet in agreement with the literature. The finding of Podocarpus sp. pollen grain, characteristic of highlander vegetation, suggests human mobility of JABII individuals which were settlement in the coast. Paleogenetic analyses showed Ascaris sp. helminth infection based on nad1 gene fragment detected from an individual excavated at L3 FS7 burial (1826 ± 40 BP). This aDNA result places the antiquity of Ascaris sp. infection, and haplotypes that are circulating in humans and other animals nowadays, in Pre-Columbian South American times.