Most Revd Justin Welby urged all sides of the of the issue not to give up on the "long road" to reconciliation.
He was speaking on a visit to the burial place of St Patrick in Downpatrick on St Patrick's Day for 50 years.
"You are a symbol of hope to so many around the world," he said, "don't give up - make it work. It is a gift of God to you for the world".
Archbishop Justin added: "It is held in your hands as a treasure."
It's more than 15 years since the Good Friday agreement which aimed to bring an end to violence between Catholic and Protestants.
Lower estimates suggest 3,800 people died and 40,000 and 100,000 people were injured in the troubles.
"Despite the difficulties, and there remain huge challenges because reconciliation is a fragile plant that always finds itself in the cold climate of the human heart, and can only be nurtured with the warmth of love, of fellowship, of mutuality of the spirit of God from whom it comes," the archbishop added.
"Despite those challenges you have embarked with enormous courage on the long road to reconciliation and you are a symbol of hope for so many around the world.
"Peace which starts from within us overflows through our communities.
"We are lights for the world to reveal the hidden sin and the prophetic calls for a new way of being, that is the politics of reconciliation and peace in Christ, not the politics we know at the minute."