Aquilegia microcentra is a species of flowering plant in the family Ranunculaceae native to Uruzgan Province in central and southeastern Afghanistan.

The species was first described by the Flora Iranica in 1992 from specimens collected by Karl Heinz Rechinger in 1967.

[2]: 104 Aquilegia microcentra was first described by Austrian botanist Karl Heinz Rechinger in 1992 within the Flora Iranica.

[2]: 104  The holotype was collected by Rechinger on July 1, 1967, in Afghanistan and is held in the herbarium of the Natural History Museum, Vienna.

The type locality was given as "Deh Kundi" and it is listed as having been collected at an elevation of 2,900 metres (9,500 ft).