Akodon is the most diverse genus of the tribe Akodontini, comprising 41 extant species. Although distributed in a wide range of environments in South America, the genus was long considered to be absent from Amazon Forest. Nonetheless, in recent decades, records of Akodon have been reported based on specimens from southern Amazonia, throughout the contact zone with Cerrado. Published data about the unique karyotype (2n=10), along with evidence of sister phylogenetic relationship (Cytb sequences) with Akodon cursor, a species from the Atlantic Forest, suggest that these specimens represent an undescribed species. Herein we hypothesize that these samples represent a new species of Akodon from Amazonia-Cerrado transitional areas. Through the analyses of 217 specimens from Mato Grosso and Pará states, Brazil, as well as 336 specimens of Akodon cursor species group from the Atlantic Forest, we provide qualitative and quantitative external and craniodental data that support their distinction in comparison with other congeners. The sister relationship between this new species and A. cursor provide additional evidence of a past connection between the two largest tropical forests of South America. Moreover, the recognition of Akodon n. sp. points to the presence of the genus in the Amazonia-Cerrado transition, an area currently under great anthropic pressure, highlighting the fact that we might be losing a portion of Brazilian biodiversity before even getting to know it.