Pachygenium muyscarum is morphologically similar to P. tamanduense (Kraenzl.) Szlach., R.González & Rutk., from which it differs by flowering without leaves (vs. flowering with leaves), labellum 1.4–1.6 cm long (vs. 1.2–1.4 cm long), apical labellum lobe trilobate (vs. entire, rounded) and labellum nectar glands 0.2–0.4 cm long (vs. up to 0.1 cm long). Terrestrial herb, 3–5 cm in height without the inflorescence and 15–30 cm in height, including the inflorescence. Roots 10–20 × 0.5–0.8 cm, fasciculate, terete, attenuating slightly towards the apex, pale dull yellowish. Leaves 6–16 × 1–2 cm, 4–6 when present, elliptic-lanceolate, 5–6 parallel nerved, base attenuate, margin entire, apex acute, dark green adaxially, pale green abaxially, forming a rosette, with the leaves ascending; pseudopetioles sublinear, channeled, white adaxially, tawny abaxially. Inflorescence 15–25 cm long, racemose, erect, glabrous below the middle, becoming increasingly villose towards the apex, hairs multicellular and clavate; peduncle 12–20 cm long; sheaths 3.7–5.0 × 0.7–1.0 cm, 5–12, lanceolate, chartaceous, yellowish green at the base, green on the rest, glabrous; floral bracts 1.8–2.5 × 0.6–0.8 cm, elliptic-lanceolate, concave, cuneate, 3–4 veined, olive green, tomentose with multicellular, clavate, caducous hairs, margins irregularly ciliate and becoming papillose near the apex. Flowers 0.8–1.4 cm long, ascending, resupinate, dorsal sepal green, lateral sepals green with the margins white, tomentose abaxially, glabrous adaxially, petals green with the apex white, labellum green at the base, white in the middle at the apex, with greenish dorsal vein. Dorsal sepal 8–1.2 × 0.4–0.6 cm, ovate-lanceolate, concave, 3–5 veined. Lateral sepals 1.2–1.4 × 0.3–0.5 cm, lanceolate-falcate, concave, 3–5 veined, base fused into a saccate nectary. Petals 1.0–1.2 × 0.2–0.3 cm, oblong, spatulate, 3–5 veined, fused internally at the base with the dorsal sepal, apex acute, external margin irregularly papillose above the middle. Labellum 1.4–1.6 × 0.4–0.6 cm, panduriform, with 3–9 veins, base provided at each side with one subulate, uncinate nectar gland, 0.2–0.4 × to 0.1 cm, apical lobe 0.4–0.6 × 0.4–0.6 cm, rounded. Column 0.8–1.2 × 0.1–0.2 cm, terete, papillose, canaliculate; anther 0.2–0.4 cm long, ellipsoid; rostellum 0.1–0.3 cm long, triangular; ovary 1.3–1.6 × 0.3–0.5 cm, fusiform, cylindrical, green, tomentose; stigma concave, slightly bilobed. Pollinarium 4.0–4.1 × 1.9–2.0 mm, wishbone-shaped, with two creamy-white pollinia; pollinia 3.0–3.2 × 0.8–1.0 mm, ellipsoid, creamywhite, viscidium 0.3–0.5 × to 0.1 cm, rhomboid, grey Capsule 1.6–1.7 cm long × 0.6–0.7 cm wide, elliptic, tomentose, with 3 longitudinal keels, perianth persistent, brown. Seeds 0.5–0.8 × 0.15–0.20 mm, seed coat spiranthoid type, with 12–15 cells in length and 5–7 in width, cells rectangular with one of both ends arched and prominent, embryo 0.25–0.30 mm, ovoid.