Boraras naevus is distinguished from its congeners with a similar blotched color pattern (viz. B. maculatus and B. micros) by pronounced sexual dimorphism of the anteriormost blotch situated on the body side, which is a small circular marking of roughly orbit size or smaller in females and a large dorso-ventrally orientated oval-shaped marking larger than the orbit in males (vs. anteriormost blotch similar in size and shape in both sexes) and by its lower number of principal caudal-fin rays (9+8 vs. 9+9 in B. micros, 9–10+9 in B. maculatus). It is further distinguished from B. maculatus by its lower number of body scales in the midlateral row (24–26 vs. 26–29), and its lower number of pelvic-fin rays (i.5.i vs. i.6.i), and from B. micros by its higher number of body scales in the midlateral row (24–26 vs. 22–23), higher number of branched dorsal-fin rays (7 vs. 5–6), the presence of red and black pigment along the anterior edge of the dorsal and anal fins of males in life (vs. all fins transparent without red or black pigmentation in life in both sexes), the presence of infraorbital 4 (vs. infraorbital 4 absent), infraorbital 2 contacting both infraorbital 1 and infraorbital 3 (vs. infraorbital 2 greatly reduced in size, without contact with adjacent infraorbital bones), and the presence of the mesocoracoid (vs. mesocoracoid absent). Boraras naevus can be distinguished from the remaining species of Boraras (B. brigittae, B. merah and B. urophthalmoides) by the absence of a midlateral stripe (vs. broad, uninterrupted midlateral stripe from upper extremity of gill opening to middle of caudal-fin base in B. brigittae and B. urophthalmoides; or narrow, frequently interrupted midlateral stripe from above anal-fin origin to middle of caudal-fin base in B. merah) (Ref. 87760).