Koufonisia is a former community in the Cyclades, Greece. Since the 2011 local government reform it is part of the municipality Naxos and Lesser Cyclades, of which it is a municipal unit.

Koufonisia includes three main islands:

• Epano, Pano or Ano Koufonisi (for Upper) often merely called Koufonisi
• Kato Koufonisi (for Lower) and
• Keros or Karos

Geographically, they are located on the south-southeast side of Naxos and on the west-northwest of Amorgos and belong to the archipelago of the Lesser East Cyclades. Uninhabited Keros is a protected archaeological site from which a large number of ancient Cycladic art pieces have been excavated in the 20th century.