Hipposideros ater has a forearm length of 39.5 and 40.3 mm, all measurements based on Myanmar material unless otherwise stated. The ears are slightly large. The noseleaf is small and have one pair of rudimentary supplementary lateral leaflets. The internarial septum is slightly inflated with the greatest width of 0.8 mm. There is a small gland behind the posterior leaf. The fourth metacarpal averages longer than the third and fifth. The baculum has a simple rounded tip and a narrow shaft; at 1.7mm.
The skull has a condylo-canine lengt of 13.5-13.7 mm and mastoid width of 8.2-8.4 mm. The rostum, in lateral profile, is horizontal. The sagittal crest is low. Each zygoma has a variebly developed jugal projection on its postereior part; although present in some specimens, in other it is scarcely evident. Upper toothrow length (C-M3) is 5.1-5.2 mm. The first upper premolar (P2) is very small and extruded from the toothrow; the second upper precanine (C1). The crown of the first lower premolar (P2) is about two-thirds of the second (P4), and about half of its height.