Habenaria lithophila flowers are small and green. The concave, lance-shaped dorsal (median) sepal, about 6 mm long, is acutely pointed, positioned over the column. The pair of lateral sepals are also lanceolate, spreading to the sides behind the lower petal lobes that are linear and curving outwards. The upper petal lobes, also linear, adhere to the sides of the dorsal sepal.
The lip is three-lobed, its surface smooth or finely hairy. The midlobe is oblong, slightly longer than the linear sidelobes. The spur, up to 11 mm long, is slender with a narrow mouth and inflated tip (Liltved and Johnson, 2012; Pooley, 1998).