Brachyhypopomus palenque is distinguished from other species of the genus Brachyhypopomus by the following combination of characters: caudal filament length 7.4-14.0% of length to end of anal fin (vs. 14.1-83.1% in B. alberti, B. batesi, B. benjamini, B. brevirostris, B. bullocki, B. cunia, B. draco, B. gauderio, B. hamiltoni, B. hendersoni, B. janeiroensis, B. jureiae, B. menezesi, B. pinnicaudatus, B. provenzanoi, B. sullivani, and B. walteri); pale stripe along middorsal region absent (vs. prominent pale uninterrupted middorsal stripe from occipital region to base of caudal filament present in B. arrayae, B. beebei, and B. belindae); mouth width 25.1-37.8% HL (vs. 15.9-23.2% in B. bennetti and B. flavipomus); accessory electric organ over the opercular region absent (vs. present in B. bombilla and B. regani); 19-22 precaudal vertebrae (vs. 24-26 in B. verdii); continuous or discontinuous dark vertical or diagonally oriented bars or saddles on body surface dorsal to lateral line absent (vs. present in B. diazi and B. palenque) (Ref. 116763).