Citing "irreconcilable differences," the couple have decided to go their separate ways though the split is thought to be friendly.
The Hollywood couple have a 17-year-old daughter, Stella, and the legal documents reveal that Melanie is asking for full custody and child support.
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As TMZ reports though, it is a "moot point" as Stella turns 18 very soon.
The pair were thought to defy conventional Hollywood short-lived unions with their long marriage, and they were often seen larking around on the red carpet together.
Their worlds collided in 1995 when both actors were cast together in the film Two Much. Melanie said it was love at first sight although she also recalled an awkward introduction. “He asked me how old I was,” she said, “That was the first thing he said to me."
After a whirlwind romance the pair divorced their respective partners and married on May 14 the following year in a private, low-key ceremony in London.
Five months pregnant when they took their vows, Melanie gave birth to their daughter Stella del Carmen on September 24, 1996.
It was Melanie's second child - she gave birth to her daughter Dakota in 1989 when she was married to Don Johnson.
The pair had also spent many years putting heir energies into philanthropy. "I think everybody who has done well out of life has to give something back," Melanie said. "We have to share and we have to help those who have nothing."
In 2002 their dedication was recognized when the couple received the Stella Adler Angel Award for their extensive charity work, and in 2003 they both took on roles on Broadway, deciding to extend their careers and try something new at the same time.