Meristogenys stigmachilus inhabits rocky streams in highland forests of Sabah. The species was described from Mahua, Crocker Range National Park, Sabah, at 1063 m elevation. It is also known from Gunung Trus Madi Sarawak at approx. 850 m.

Within the genus, M. stigmachilus is a relatively large species with snout-vent length 43–50 mm in males, female measure 69–79 mm.

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 (name-giving feature). 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. More research has to be done on basic ecological parameters of the species' ecology. 

The tadpole have the typical and easy to recognize appearance of a Meristogeny tadpole, including a streamlined body, a strong tail and a large belly sucker. There are three uninterrupted and four interrupted keratodont rows on the upper lip. The lower lip bears six keratodont rows of which the first (close to the jaw) is divided. The head and trunk unit possesses four pairs of glandular clusters: a postorbital cluster about an eye length behind eye (3–4 glands); an infraorbital cluster at the base of the snout (3–6 glands); a prespiracular cluster just anterior to spiracle(3–7 glands); a midlateral at the posterior end of body(2–5 glands). The dorsal fin is without glands, however ventral fin glands are present (1–14 glands). The head and the trunk are scattered dorsally with minute protuberances, anterior to eye in older larvae.