Distinguished from Microlepidogaster perforatus and Microlepidogaster longicolla by having first dorsal-fin proximal radial attached to the neural spine of seventh vertebra, with posterior portion contacting also the eighth centrum (vs. first dorsal-fin proximal radial attached to the neural spine of eighth or ninth vertebra in Microlepidogaster perforatus, and to the neural spine of tenth or eleventh vertebra in Microlepidogaster longicolla); 29-30 vertebrae (vs. 31 in Microlepidogaster perforatus and 31-33 in Microlepidogaster longicolla); 18-21 mid-dorsal plates (vs. 9-13 in Microlepidogaster perforatus, and 13-17 in Microlepidogaster longicolla); deeper caudal peduncle (10.0-11.4% in SL vs. 7.7-8.5% in Microlepidogaster perforatus, and 5.4-7.3% in Microlepidogaster longicolla); greater distance between dorsal-fin origin and anal-fin insertion (19.4-23.8% in SL vs. 16.4-18.8% in Microlepidogaster perforatus, and 14.7-16.2% in Microlepidogaster longicolla); and nostril width markedly wider in males than in females (vs. approximately equivalent in size for both sexes, slightly wider in males than in females in Microlepidogaster perforatus, and equivalent in size for both sexes in Microlepidogaster longicolla). Can be also diagnosed Microlepidogaster perforatus by presence of the iris operculum (vs. absence); median plate series complete to caudal peduncle end (vs. median plate series truncated, with last two plates of dorsal and ventral series contacting in midline); greater head depth (43.4-53.1% vs. 40.7-42.3% in HL); greater orbital diameter (13.6-18.5% vs. 11.1-13.5% in HL); pelvic-fin first unbranched ray longer in males than in females (vs. equivalent in size in both sexes); and supraneural without paired anterior processes (vs. processes present). Also differs from Microlepidogaster longicolla by having anterior margin of snout with a paired rostral plate (vs. snout with small plates, naked in the anterior margin); by pectoral-fin axillary slit present only in juvenile specimens); longer pectoral-fin unbranched ray (20.0-23.8% vs. 13.4-16.2% in SL in Microlepidogaster longicolla (Ref. 86675)).

Description: Dorsal fin ii, 6-7; anal fin i, 4-6; pectoral fin i, 6-7; pelvic fin i, 5-6 (Ref. 86675).