Badis autumnum is distinguished from all other congeners by its color pattern consisting of two autapomorphies. It can be diagnosed from all members of the B. badis group (B. badis, B. chittagongis, B. dibruensis, B. ferrarisi, B. kanabos, B. soraya and B. tuivaiei) by the absence of a blotch on the superficial part of the cleithrum above pectoral-fin base; from all members of the B. assamensis group (B. assamensis and B. blosyrus) by the absence of a posterodorsal opercular blotch and the absence of two parallel rows of dark spots and alternating light and dark stripes along its physique; from all species of the B. ruber group (B. khwae, B. ruber and B. siamensis) by the absence of a cleithral blotch and absence of a blotch on the dorsolateral aspect of the caudal peduncle; from all members of the B. corycaeus group (B. corycaeus and B. pyema) by the absence of an ocellus on the caudal-fin base; from B. kyar by the presence of a conspicuous median black blotch on the caudal peduncle; from B. singenensis by the absence of a posterodorsal opercle blotch and absence of three dorsal-fin blotches and a single round blotch on the anal-fin base; from B. juergenschmidti by the absence of white margins on dorsal and ventral aspects of the caudal fin in males and presence of a strongly curved caudal-fin base bar; and from B. britzi by the presence of a conspicuous median black blotch on the caudal peduncle. It is very similar to B. andrewraoi and B. kyanos in color pattern, from which it can be distinguished by two unique characters that also distinguish it from all congeners: presence of a blotch above the base of the opercular spine, and of a conspicuous dark blotch on pectoral-fin base. It also differs from B. kyanos in having 16-18 scales around caudal peduncle (vs. 18-19). In addition, it can be diagnosed from all congeners by the presence of a black caudal-fin margin, outlining entire fin; and from B. andrewraoi by having 16-18 scales around caudal peduncle (vs. 18) (Ref. 103291).