The flower of Moraea polystachya is deep blue or violet, occasionally white. The inflorescence may be unbranched or much branched with several short-lived flowers.

The outer tepals are notably larger than the inner three, marked at the base by yellow to orange nectar guides. Dark blue, straight veins radiate out from the nectar guides to the tepal margins. The tepals often droop. Their margins are variable in shape. The inner tepals are paddle-shaped and similarly dark veined, but lacking the yellow markings. The style branches are erect, flattened and petal-like while split at their tips (Manning, 2009; Vahrmeijer, 1981).