Parotocinclus halbothi can be diagnosed from other species of the genus from northeastern to southeastern Brazilian rivers and the río de La Plata basin by its cheek canal plate elongated posteriorly on the ventral surface of head and contacting the cleithrum (vs. canal plate not elongated posteriorly and not contacting the pectoral girdle). It is distinguished from its congeners from the Guianas, Orinoco, and Amazon basins, except Parotocinclus collinsae , by its lack of triangular patch of dark pigmentation on the anterior portion of dorsal-fin membrane (vs. present), by having unicuspid accessory teeth on both the premaxilla and dentary (vs. absent), and by its lack of Y-shaped light mark on the snout and head (vs. present). It differs from P. collinsae in having the small, circular, median abdominal plates arranged in 4 to 7 irregular longitudinal series (vs. median abdominal plates transversely elongated and arranged in one longitudinal series), the snout and rostrum pigmentation in a dorsal view not reticulated and without dark dots on the dorsolateral surface of head (vs. snout and rostrum pigmentation reticulated and with dark dots present on head), and by the rudimentary adipose fin without a membrane (vs. with obvious adipose fin having hyaline membrane) (Ref. 95582).