Mystacidium flanaganii is a dwarf epiphytic orchid that grows to 4 cm. Its roots, visible for inspection, are few and thin, 1 mm in diameter, growing in a zigzag pattern.

The leaves are strap-shaped or elliptic, sometimes slightly curved. There are from two to five of them, from 15 mm to 30 mm long and 5 mm to 7 mm wide.

The distribution of M. flanaganii, a South African endemic, lies in the east of the country, from the Eastern Cape through KwaZulu-Natal to Mpumalanga, at elevations up to 1800 m.

The habitat is margins of cool, moist forests in light to heavy shade. The plants are found on branches and twigs of trees and shrubs. The species is not considered to be threatened in its habitat early in the twenty first century (Pooley, 1998; www.africanorchids.dk; www.redlist.sanbi.org).