Creteuchiloglanis brachypterus is distinguished from C. gongshanensis, by having the pectoral-fin length 65.8–78.7% Pt–Pl distance (vs. 95.3–99.6%), a shorter caudal fin (11.2–12.9% SL vs. 14.7–17.8%), a shorter pectoral fin (18.5–21.8% SL vs. 25.3–28.1%), a shorter pelvic fin (14.5–18.7% SL vs. 19.2–22.2%), a larger eye (7.0–12.0% HL vs. 5.8–6.7%), and a deeper caudal peduncle (35.8–43.7% caudal-peduncle length vs. 23.5–29.7%; 6.5–8.0% SL vs. 3.8–4.6%). It is distinguished from C. kamengensis by having a shorter caudal fin (11.2–12.9% SL vs. 13.8–16.6%), a shorter pectoral fin (18.5–21.8% SL vs. 25.0–28.7%), a larger eye (7.0–12.0% HL vs. 5.1–6.4%), a shorter prepectoral length (10.0–16.1% SL vs. 16.9–17.5%), a longer post-adipose distance (9.1–11.3% SL vs. 8.2–8.8%), and by the presence (vs. absence) of pale patches on the body. Creteuchiloglanis brachypterus is distinguished from C. longipectoralis by having the pectoral-fin length 65.8–78.7% Pt–Pl distance (vs. 98.1–120.9%), i,6 dorsal-fin rays (vs. i,5), a deeper body, body depth at anus (9.6–11.8% SL vs. 7.8–8.1%), a deeper head depth (9.0–11.8% SL vs. 7.2–8.8%), a longer post-adipose distance (9.1–11.3% SL vs. 7.0–8.9%), and by the presence (vs. absence) of pale patches on the body. It is distinguished from C. macropterus by having the pectoral-fin length 65.8–78.7% Pt–Pl distance (vs. 81.4–99.8%), pelvic-fin length 46.1–59.4% Pl–A distance (vs. 60.0–66.5%), a shorter caudal fin (11.2–12.9% SL vs. 14.2–19.9%), a shorter pectoral fin (18.5–21.8% SL vs. 22.6–28.5%), and head depth 9.0–11.8% SL (vs. 13.0–14.5%) (Ref. 87311).