The Hypancistrus genus is recognized in the Río Orinoco basin and Rio Xingu in the Guiana and Brazilian Shields, respectively. Some of its species are important in ornamental fishing. Despite this significance, many other undescribed species are still awaiting to be named. Here we describe a new species of Hypancistrus found on bedrock in the Rio Tocantins, representing an extension of the distribution of the genus. Also, a multigene phylogeny is presented to evaluate the taxonomic position of this species concerning congeners. The new species differs from all congeners by (1) hypertrophied odontodes on cheeks reaching beyond the cleithrum, (2) a supraoccipital crest conspicuously elevated, (3) a supraorbital crest slightly convex, (4) oblique bars on the anterior part of the body, (5) a dark E-shaped mark on the snout, (6) three oblique dark bars on the anterior part of the body and horizontal vermicular bars from the pectoral girdle to the posterior insertion of the dorsal fin, (7) a thin light gray bar on the posterior of the head extending across the branchial opening, (8) a tan background color, (9) a developed suspensorium with a diminished appendix in the metapterygoid, and (10) a dentary plate robust significantly fused with the angulo-articular bone. The molecular phylogenetic results show the new species forming a group with Hypancistrus zebra (Brazilian Shield-Rio Xingu) as a clade, a sister group of a monophyletic group consisting of all congeners from the Río Orinoco.