The Solimões Formation (Eocene-Pliocene) is a well-known geological unit due to the great diversity of crocodylian species. Here we describe a new species of Melanosuchus, M. latrubessei sp. nov., from the Talismã locality, state of Amazonas, from the Upper Miocene of the Solimões Formation (Solimões Basin, Brazil). A new phylogenetic inference focused on Caimaninae is provided and the different evolutionary scenarios involving this new species are discussed. In addition, quantitative morphology studies are carried out and comments regarding the paleoecology aspects of this new species are made. M. latrubessei represents a medium-sized generalist predator, being proportional to the medium-sized M. niger. This new species inhabited the drainages of the Solimões Formation and was ecologically related to other taxa of crocodylians during the proto-Amazon Miocene. The evolutionary advantages of Melanosuchus genus are discussed to better understand the biogeographical occurrence of M. niger in South America, a species which survives to this day in contrast to several other species that became extinct during the Miocene-Pliocene periods. The extinction of the Miocene-Pliocene crocodylian taxa of the Solimões Formation, including Melanosuchus latrubessei, seems to be directly related with the uplift of the northern portions of the Andes, which generated significantly changes in drainages and Amazon paleoenvironments.