Distinguished from all congeners except Crenicichla jurubi, C. semifasciata, and C. yaha by its stout lower pharyngeal tooth plate with molariform teeth (vs. slender pharyngeal tooth plate without molariform teeth). Differs from C. jurubi in having a serrated preopercle (vs. smooth), a well developed suborbital stripe (vs. absent or reduced to a spot at margin of orbit), and lacking scattered dots on back and sides (vs. presence); from C. semifasciata in having an ascending arm of the premaxilla longer (vs. shorter than the dentigerous one), caudal fins subtruncated (vs. deeply rounded), caudal fin scaled only on its basal third (vs. mostly scaled), caudal spot without light ring (vs. caudal spot surrounded by a silvery or orange ring), and a narrower interorbital width (17.1-23.3% vs. 32.0-40.0% of HL); and from C. yaha by having a stouter lower pharyngeal tooth plate with about 16 molariform teeth (vs. about 4 molariform teeth), and absence of microbranchiospines on gill arches (vs. presence).

Differs further from other species inhabiting the rio Parana basin by the following characters: from C. iguassuensis and C. tesay) in having isognathous jaws (vs. lower jaw prognathous); from C. hu in having a color pattern with a gray or olive green background (vs. dark brown to black), and E1 row scales 54-60 (vs. 47-54 ); from C. mandelburgeri in having more scales in E1 row scales (54-60 vs. 44-56), jaws isognathous (vs. lower jaws prognathous), and absence of lateral band in adults (vs. presence); from C. ypo in having isognathous jaws and blotches on flanks placed below the upper lateral line (vs. lower jaw slightly prognathous and the blotches are extending 3 to 4 scale rows above and below lateral line); and from C. haroldo by lacking brown dots on each lateral line scale and lateral band on flanks (vs. present in C. haroldoi). The absence of a lateral band separates C. taikyra from C. jaguarensis. Crenicichla jupiaensis can be diagnosed from C. taikyra in having the suborbital stripe reduced to a few spots posterior to the orbit, a thin black line on the posterior margin of preoperculum, cheek naked, and numerous vertical stripes. Crenicichla lepidota and C. britskii have a humeral spot (vs. absent in C. taikyra). Crenicichla scottii has parallel and thin longitudinal bands and C. gillmorlisi has small dark dots all over the sides, features not present in C. taikyra. Crenicichla vittata has 78-85 in E1 row scales, lateral band, and a particular color pattern on top of the head forming a crown design whereas C. taikyra has 54-60 E1 row scales, absence of lateral band, and the pattern of pigmentation on head described above (Ref. 94256).