BELFAST, Northern Ireland — In a moment of heady symbolism that would once have seemed unthinkable, Queen Elizabeth II,Britain’s head of state, shook hands on Wednesday with Martin McGuinness, a onetime commander of the Irish Republican Armyopposed to everything she stands for.

The gesture represented a remarkable sign of reconciliation for both figures, since the queen is the titular head of Britain’s armed forces — the sworn enemy of the I.R.A. throughout the three decades of sectarian strife known as the Troubles. Her cousin, Lord Mountbatten, was killed in an I.R.A. attack on his yacht off the west coast of Ireland in 1979.

The handshake came 13 months after the Queen paid a groundbreaking visit to the Irish Republic designed to heal decades of hostility that have gradually given way to a less freighted relationship following joint British and Irish efforts to cement the 1997 cease-fire in Northern Ireland.

But after the queen arrived in Belfast on Tuesday, police fought running battles with youths throwing Molotov cocktails in the republican Broadway area of the city, recalling lingering hostilities between the mainly Protestant Unionists who seek closer ties to mainland Britain and the mainly Roman Catholic Republicans seeking a united Ireland. Nine officers suffered minor injuries, police officials said. The violence reflected continued divisions in a city carved into sectarian zones by barriers and so-called peace walls between neighborhoods.