Limited knowledge of the geographical distribution of brocket deer persists due to their elusive behavior and the morphological similarity among species. A population of red brocket deer from the genus Mazama was recently found in a protected area of the Brazilian Atlantic Forest, the Rio Doce State Park (Brazilian acronym PERD), but identification to species level was not available. Since the Atlantic Forest harbors two endemic and threatened red brocket deer, this study aimed to identify which species occur in PERD through fecal DNA analysis. Fecal samples collected in PERD and throughout the Atlantic Forest were sequenced for six mitochondrial DNA region fragments (1450bp) and analyzed towards a group of reference specimens. We performed phylogenetic analyses and implemented coalescent methods of molecular species delimitation (GMYC and bPTP) to identify molecular operational taxonomic units (MOTUs). We also constructed a haplotype network and a genetic distance matrix. The phylogenetic hypothesis recovered the samples from PERD linked to the Small Red Brocket deer ( Mazama jucunda), but in a reciprocally monophyletic topology, corresponding to two exclusive MOTUs. PERD has unique haplotypes and its genetic distance to M. jucunda is similar to that between M. jucunda and its most closely related species, the Brazilian Dwarf Brocket ( Mazama nana). Herein we report an evolutionary significant unit (ESU) of M. jucunda 700 km apart from the species current distribution. The observed genetic structure and the isolation context of PERD raise the hypothesis of a new red brocket species that should be further tested, including cytogenetic data. This study represents an important advance in the knowledge of the geographical distribution and genetic structure of a threatened Neotropical forest deer endemic to a devasted hotspot with direct and short-term implications for its conservation.