Phoxinus karsticus is distinguished from other congeners from Italy and Western Balkans by having high number of scales in longitudinal series 81-86, and number of circumpeduncular scales, 40-42, size of about 91 mm of TL. The holotype has a longitudinal band discolored or reduced. The holotype, and paratypes have patches of breast scales well developed and united in their third front. Dorsal fin has three simple rays and 7-8 branched rays; 8 branched rays only seldom were found in all others sample here analyzed; the pharyngeal teeth formula from left bone is 5.2 or 4.2. One additional non-unique character useful to distinguish the species is the anterior origin of anal fin placed in advance of vertical through posterior insertion of dorsal fin, reaching the level of the fifth or sixth branched rays of the dorsal fin (Ref. 105385).