Meristogenys stigmachilus inhabits rocky streams in highland forests of Sabah. Snout-vent length 43–50 mm in males, female measure 69–79 mm.
The species has been described from Crocker Range National Park, Sabah, at 1.200 m elevation. It is also known from Gunung Trus Madi Sarawak.
The fourth toe is fully webbed to disk of the toe. The back side is light brown dotted with dark brown. It bears dark spots on upper and lower lips. The iris is bicoloured, pale yellowish green above and pale brown below, with a small portion of reddish orange in between; a small light circle on the centre of a tympanum; The limbs are marked above with alternating light- and dark- brown crossbars. The rear of the thighs are light brown with scattered light dots.
The throat and chest are whitish with dots of melanophores; abdomen whitish. The ventral surfaces of the legs are whitish, with dense dots of melanophores.
At the type locality, larvae were seen in a river of width 3–5 m, but it is not yet certain if this environment is the typical larval habitat.