The fragrant flowers of Habenaria anguiceps grow in a many-flowered spike of about 8 cm in length, or if the flowers really have pedicels as some descriptions say, in racemes. The dorsal sepal is ovate, forming a pointed hood with the two olive-green lateral petals positioned as walls around the margins of the dorsal sepal, nearly to its tip. The two lateral sepals, positioned obliquely and tapering to narrow tips, are channelled and curving both sideways and backwards. The lip below resembles a tongue and points downwards. It is long, oblong and fleshy, coloured darkly olive-green with a rounded tip. The spur is club-shaped.

Flowering starts in late spring, continuing through summer. The flowers in picture were photographed in January (iSpot; JSTOR; www.orchidspecies.com).