Schistura scyphovecteta can be diagnosed from all congeners by the combination of

the following characters: lateral line with six dark brown saddles, each one continuing to the flank, forming globular-shaped bars overlaying a hazy brown stripe; a complete lateral line; dorsal-fin base with two black spots; an incomplete black basicaudal bar; absence of median notch on the lower jaw; and males with a suborbital flap. This new species is similar to its congener S. menanensis from the Mae Nam Nan drainage, Thailand by possessing a longitudinal brown stripe along the lateral line superposed by the bar pattern, but differs from that species in

having a complete lateral line (vs. incomplete lateral line), dorsal fin with 7½ branched rays (vs. 8½), pectoral fin with 10 branched rays (vs. 9), and the absence of a median notch on the lower jaw (vs. presence) (Ref. 94459).