We describe a new species of microhylid frog of the genus Synapturanus from the lower Putumayo basin in Loreto, Perú. Specimens inhabited the soils of stunted pole forests growing on peat. The new species is distinguished from other species of Synapturanus through morphology, genetics, and acoustic characteristics. This species differs from most nominal congeners by having a head flat in lateral view (vs convex in the rest of species), a characteristic only shared by S. rabus and S. salseri. The new species can be distinguished from S. rabus and S. salseri by a combination of morphological characters and by having an advertisement call with a note length of 0.05–0.06 seconds (vs 0.03 seconds in S. rabus) and a dominant frequency ranging from 1.73 to 1.81 kHz (vs 1.10–1.47 kHz in S. salseri). Principal component analyses of 12 morphological characters and three acoustic variables further support differences between the new species and its described and undescribed congeners.