Stenogyne microphylla is a scandent vine that can grow several meters long and become woody at the base. The stems are 4-angled and may be glabrous or densely hispid, with retrorse hairs sometimes restricted to the stem angles. The leaves are simple, opposite, and ovate to elliptic, measuring 0.4–1.3(–2.7) cm long and 0.2–0.9(–1.5) cm wide. The apex is acute or obtuse, while the base varies from attenuate and acute to obtuse or truncate. The surfaces are either glabrous or densely hispid, and the blades are membranous. The margins are crenate or lobed. Petioles are 1–6(–13) mm long and range from sparsely to densely hispid. Stipules are absent. The flowers are arranged in clusters of 2(–6) per verticillaster, axillary, with pedicels measuring 1.5–3.5 mm long and ranging from glabrous to hispid. The calyx is slightly bilaterally symmetrical, campanulate, and 3.5–8 mm long, enlarging in fruit. The upper lip is 3-lobed, while the lower lip is 2-lobed, with the teeth measuring 1–4 mm long and 1–2 mm wide at the base and may split longitudinally. The corolla is bilabiate, with a greenish-yellow tube and brownish-green to pinkish-brown lobes. The exterior is tomentose, while the interior is glabrous. The corolla tube is narrowly funnelform and slightly falcate, measuring 10–14 mm long. The upper lip is 5–8 mm long, either entire or 2-lobed, while the lower lip is 1–3 mm long with 3 ovate lobes of similar size, sometimes with revolute margins. The distal portion of the corolla is sparse to densely pubescent externally, with simple or multicellular hairs, sometimes glandular-pubescent within. A nectary disk is often present at the base of the ovary, either annular or developed on the anterior side only. It has four stamens, with both pairs being similar in length or slightly longer upper pair. The stamens are either included within the corolla or well-exserted beyond the upper lip. The filaments are inserted near the throat and pubescent. The anthers are dithecal, with divaricate sacs that open by longitudinal slits. The ovary is superior, with two longitudinally divided carpels containing one ovule per lobe with basal-axile placentation. The style is exserted, arising between the lobes, and usually cleft, diverging after anther dehiscence into two short, subulate lobes. The stigmas are two-lobed. The fruit is a drupaceous, one-seeded nutlet measuring about 3–3.5 mm long. The nutlets are black at maturity, with slightly winged margins and an obliquely attached base, enclosed within the calyx at maturity. The exocarp is fleshy, and the nutlets are obovoid. The seeds contain scanty or no endosperm with an oily texture. It is found in subalpine forests between 1,200-2,700 meters.