A new killifish species, Rivulus duckensis, is described from the Reserva Adolpho Ducke, Manaus, Amazonas, Brazil. It is distinguished from other central Amazonian Rivulus species by maximum body size, adult color pattern, habitat preference and mitochondrial DNA sequences. Based on the phylogenetic analysis of molecular sequence data, our best hypothesis suggests that R. duckensis is sister taxon to a clade of Rivulus species occurring in the upper Río Orinoco basin, Amazonas state, Venezuela and Rivulus rectocaudatus, Amazonas department, Peru.