Although the Atlantic Forest marmosets (Callithrixspp.) are among the best studied Neotropical primates, the Amazonian marmosets (Callibella humilis, Cebuellaspp. andMicospp.) are much less well-known. Even species diversity and distributions are yet to be properly determined because field data and materials currently available in scientific collections do not allow comprehensive taxonomic studies of Amazonian marmosets. From 2015 to 2018, we conducted 10 expeditions in key-areas within southern Amazonia where little or no information on marmosets was available. In one such region—the Tapajós–Jamanxim interfluve—we recorded marmosets with a distinctive pelage pigmentation pattern suggesting they could represent a new species. We tested this hypothesis using an integrative taxonomic framework that included phylogenomic data (ddRAD sequences), pelage pigmentation characters, and distribution records. We found that the marmosets of the northern Tapajós–Jamanxim interfluve have unique states in pelage pigmentation characters, form a clade (100% support) in our Bayesian and Maximum-Likelihood phylogenies, and occur in an area isolated from other taxa by rivers. The integration of these lines of evidence leads us to describe a new marmoset species in the genusMico, named after the Munduruku Amerindians of the Tapajós–Jamanxim interfluve, southwest of Pará State, Brazil.