Writing on the Daily Beast website, Bishop Robinson said he was “forever grateful” to Mark Andrew and that details of their split were private.
The pair were married in a civil ceremony in 2003.
Gene Robinson’s ordination as a bishop of the New Hampshire diocese in 2003 divided the global Anglican communion.
In the US, hundreds of parishes broke away from the Episcopal Church – the US branch of Anglicanism – in protest, forming a new Anglican Church in North America.
The bishop became a symbol of the LGBT rights movement and an advocate for equal marriage.
In his letter, Bishop Robinson, who retired in 2012, said it was “a small comfort” to know that gay and lesbian couples “are subject to the same complications and hardships that afflict marriages between heterosexual couples”.
“My belief in marriage is undiminished by the reality of divorcing someone I have loved for a very long time, and will continue to love even as we separate,” he said. “Love can endure, even if a marriage cannot.”
Bishop Robinson, 66, had previously been married to a woman with whom he had two children. They divorced amicably in 1985 over his sexuality.