In the papers, filed by Penn on Friday, April 24 in Marin County, Calif., and obtained by Access Hollywood, the actor cites "irreconcilable differences" as the reason for the split.
Penn is also seeking to "terminate the court's jurisdiction to award spousal support" to Wright.
According to Penn's attorney, Mindy Ross, the actor did not file for divorce, but rather a "legal separation."
While the court can still rule on details including division of property and custody of children, the couple is still legally married, Ross noted.
Wright now has 30 days to also file a legal separation of marriage, or she can opt to file for divorce, which would then be granted, according to Ross.
The Oscar winner and Wright tied the knot on April 27, 1996. The couple has two children – daughter Dylan Francis, 18, and son Hopper Jack, 15.
Penn, 47, and Wright, 43, previously filed for separation in December 2007. However, they reconciled in April 2008.
Following his Oscar win in 2009 for Best Actor for his role in "Milk," Penn received a bit of backlash after leaving his wife out of his acceptance speech.
However, at the Governor's Ball later that night, Penn said he and Wright had talked about his speech prior to the show.
"She knows… She knows," Penn said at the time, explaining that the couple had discussed it ahead of time.
Wright also commented, noting they both knew there wouldn't be "enough time" to mention everyone.
The Hollywood couple has starred in several films together, including 1988's "Hurlyburly" and 1997's "She's So Lovely."
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