Phoxinus likai is distinguished from other congeners Phoxinus phoxinus, P. apollonicus, P. karsticus and P. ketmaieri by having patches of breast scales united and continuous across breast, except P. karsticus, where they are united only on anterior part. It differs also from P. karsticus by having 72-79 scales in longitudinal series (vs. 82-87 in P. karsticus) and 30-32 circumpeduncular scales (vs. 40-42 in P. karsticus). Other non-unique characters useful for the identification include:

pharyngeal teeth formula, 5.2 or 4.2, shared with P. phoxinus but not P. apollonicus; pored lateral line nearly complete, reaching almost the end of the caudal peduncle, (do not reach more than half of the length of caudal peduncle in P. ketmaieri and P. phoxinus); eye large, its diameter more than the preorbital distance, but less in the other species; snout short and blunt; longitudinal band from tip of snout to caudal peduncle where it forms a roundish spot; the band is more evident in the second half of the body; the flanks have 12-14 mid-lateral row of vertical elliptic blocks, more evident on the second half of body; anterior origin of anal fin placed at same level of vertical through posterior insertion of dorsal fin (Ref. 105385).