This species is diagnosed from all congeners, except Ituglanis paraguassuensis, by the following characters: 36 vertebrae (vs. 38 or more in all other Ituglanis, except in I. paraguassuensis, I. nebulosus, I. bambui, I. epikarsticus, I. ramiroi, and I. passensis;

unknown for I. guayaberensis); 5-6 ribs (vs. 2 or 3 in I. amazonicus, I. eichorniarum, I. gracilior, I. ina, I. macunaima, I. nebulosus, and I. parkoi ; 4 in I. laticeps and I. cahyensis; 7 in I. passensis); i,6 pectoral-fin rays (vs. i,4 in I. cahyensis, I. macunaima, and I. parahybae ; i,5 in I. amazonicus, I. eichorniarum, I. metae, and I. nebulosus; i,7 in I. bambui, I. epikarsticus, I. mambai, I. passensis; iii,5 in I. guayaberensis; i,8 in I. ramiroi); and irregular brown blotches covering the skin (vs. distinct color pattern in all other Ituglanis; absence in I. ina and the subterranean species, I. bambui, I. passensis, I. epikarsticus, and I. ramiroi). Ituglanis agreste is also easily distinguished from the subterranean species by its large eyes (vs. minute eyes) and intense pigmentation (vs. pigmentation absent or almost lack); and from its geographically closest species I. paraguassuensis by having 26-30 odontodes in an elongate interopercle patch (vs. reduced with 14-15 odontodes); seven branchiostegal rays (vs. 8) and pore s1 lacking (vs. s1 present) (Ref. 94155).