The ‘Critically Endangered’ Cone-billed Tanager Conothraupis mesoleuca was described in 1939, based on a single specimen collected in the state of Mato Grosso, western Brazil. Not seen again in the wild until 2003, this poorly-known species was rediscovered in Emas National Park, in the Brazilian state of Goiás. We describe here the discovery of a new population of Cone-billed Tanager in Chapada dos Parecis, along the upper Juruena River basin, in the state of Mato Grosso. The birds were always detected in (or near) flooded habitats along rivers. At least 40 individuals were found, but the population may be larger, since areas of potential habitat are available in the upper Juruena basin and these have not yet been surveyed. We also provide here the first information on the biology and behaviour of the species based on observations in Juruena and Emas, as well as a first description of the female. Historical documents and our records support our suggestion that “Juruena”, i.e. the type locality of the Cone-billed Tanager, refers to the Juruena telegraph station (12°50’S, 58°55’W). Considering that the range of the species is being settled, research on different aspects of its biology are urgent.