In 2016, Marquinhos was named in the Brazilian squad for the Copa América Centenario in the United States, an "experimental" selection lacking his Paris Saint-Germain defensive partners Thiago Silva and David Luiz. He played in the first two games at centre-back alongside Gil before being replaced by Miranda for the last group game, a 1–0 loss to Peru at Gillette Stadium that eliminated his team. Later that year, he was included in the squad for the team's hosting of the Olympic tournament, and in the semi-final against Honduras in Rio de Janeiro, he scored in an eventual 6–0 win.