Marsh rats of the genus Holochilus are broadly distributed and inhabit several distinct environments throughout South America. As an enigmatic group with a somewhat uncertain taxonomy, the composition and names of taxa have shifted throughout history, including the boundaries of Holochilus sciureus, a species formerly distributed in the lowlands of the Guianas, Peru, Bolivia, and northern, central, and northeastern of Brazil. Based on a combination of morphological and morphometric traits, and genomic sequences, we redefined species boundaries and split this wide concept of H. sciureus into three separated species, including a redefined H. sciureus, the newly erected from synonymy H. nanus, and an unnamed taxon. We describe this unnamed species, and provide emended diagnoses for the two redefined species. The newly named taxon inhabits the northeastern part of Brazil and differs from the other congeners by a unique combination of phenotypic and genomic characters.