Simmons, 37, and Hounsou, 48, first began dating after Simmons split from husband Russell Simmons in 2007. Their divorce was finalized in 2009.
"There have been quite a few hurtful rumors circulating," Simmons wrote on Twitter Wednesday. "The truth is Djimon+I have been separated for some time. We have remained happy, loving, co-parenting friends+family. We all have much to be thankful for."
Though never married, Simmons and Hounsou have one child together, Kenzo Lee Hounsou, 3. Simmons also has two daughters Ming, 12, and Aoki, 10, with her ex-husband.
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