Otocinclus juruenae is distinguished from all congeners, except O. cocama, by having a complete lateral line, without gap plates. It differs from O. bororo, O. caxarari, O. hoppei, O. huaorani, O. macrospilus, O. mariae, O. mura, O. vestitus, and O. vittatus (previously assigned by Schaefer, 1997 to the 'orbis clade') as well as O. batmani and O. cocama by the presence of iris operculum (vs. absence). It can be further diagnosed from all its congeners, with the exception of O. flexilis and O. xakriaba, by the coloration of the lateral trunk consisting of a series of three to four diffuse pigment blotches without a distinct midlateral stripe (vs. trunk with distinct midlateral stripe) (Ref. 110382).

Description: Dorsal-fin branched rays 7; anal-fin branched rays 5; pectoral-fin branched rays 6; pelvic-fin branched rays 5 (Ref. 110382).