Soldiers allegedly raped and sexually abused women during the crackdown
The European Union has imposed an arms embargo on Guinea and sanctions against its military leaders.
The EU said there had been a gross violation of human rights when troops opened fire on protesters last month.
Rights groups say 157 protesters died and many others were raped and beaten. Officials say about 57 people died.
The demonstrators were angry at rumours that Capt Moussa Dadis Camara, who took power in a coup last December, intended to stand for president next year.
Earlier this month the EU's development chief Karel de Gucht said the coup leader should be put on trial for crimes against humanity.
The International Criminal Court (ICC) has opened an investigation into the deaths and a UN inquiry is also under way.
West Africa's regional economic body Ecowas has already imposed an arms embargo on Guinea over the killings.
EU foreign ministers agreed on the sanctions for Capt Camara and his ruling Council for Democracy and Development (CNDD) at a meeting in Luxembourg.
The sanctions are to target "members of the CNDD and individual associated with them, responsible for the violent crackdown or the political stalemate", an EU statement said.
Guinea's previous government was overthrown in a bloodless coup last December after the death of Lansana Conte, who had ruled the country since 1984.