A new species of the eleotrid genus Microphilypus from the Upper Rio Negro basin is described herein. It differs from all congeners in the presence of 5–6 arched rows of melanophores on the abdominal region, posterior to the base of the pelvic fins, followed by six large irregularly oval black blotches, with the tips of the three posteriormost blotches visible in lateral view; a dark teardrop-shaped blotch on the caudal peduncle, extending to the base of the ventral caudal rays; five light brown blotches along the dorsal profile of the body, between the origin of the second dorsal fin and the caudal peduncle; and the poorly developed laterosensory system on the head, with horizontal rows of head papillae b and d absent. A key to the species of Microphilypnus is presented.