Rhizome 30–40 × 10–13 mm, fleshy, white, sparsely hairy, with sparse, triangular, sterile bracts. Flower stem 40–60 mm long, tapered, with scattered bracts. Flowerhead 20–25 mm wide, concave, fleshy, outer (sterile) bracts incurved, overlapping and forming a cover over the flowers. Sterile sheathing bracts surrounding the flowerhead 6–12, 3-veined, 20–35 × 5–8 mm, overlapping, cream to pinkish or violet, tips purple. Floral bracts subtending flowers long, 1-veined. Flowers 8–100, in a tight spiral, 5–6 × 5 mm, dark maroon. Sepals and petals triangular, joined in basal half, apical parts free but overlapping. Labellum narrowly heart-shaped, 1.5–2 × 1.5 mm, strongly curved, fleshy, deeply grooved, smooth; margins and tip dark red. Fruit a drupe, yellow, containing 20–150 seeds.
All sites of Rhizanthella gardneri discovered to date have an annual rainfall of 300–400 mm per annum which falls mainly in winter. Vegetation types include mallee heath, mallee scrub and, less commonly, woodland. The dominant shrubs in these communities are species of broombush (Melaleuca hamata, M. scalena and M. uncinata) which grow in extensive thickets. Rhizanthella gardneri is usually found in thickets of M. scalena, growing near creek lines. The vast majority (if not all) of the orchid plants discovered to date have been growing within 10–30 cm of a living broombush lignotuber at a depth of about 10 cm. The soils are mainly freely draining, sandy clay or sandy loam that become yellow with depth.
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