The Most Rev Justin Welby told LBC that hundreds of Christians in Africa had been killed by people who associated Christianity with homosexuality.
He warned the same could happen if the Church of England backed gay unions.
Same-sex marriage became legal in England and Wales last week, but is not supported by the Church.
Speaking on his first live phone-in on LBC Radio, Archbishop Welby recalled visiting a grave in South Sudan where 369 people had been buried.
He said the victims had been killed because local people believed allowing a Christian community to exist would mean “we would all be made to become homosexual”.
“That burns itself into your soul”, he said. “As does the suffering of gay people in this country.”
He also spoke of visiting a group of Christians in Africa who had been attacked because of policies of churches in America.
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