Aniston,49, and Theroux,46, had tied the knot in 2015 after four years of dating. They had met on the sets of the film "Wanderlust" in 2011.
In a statement released through Aniston's publicist Stephen Huvane, the couple said the decision to split "was mutual and lovingly made at the end of last year", according to Entertainment Weekly.
"In an effort to reduce any further speculation, we have decided to announce our separation. This decision was mutual and lovingly made at the end of last year. We are two best friends who have decided to part ways as a couple, but look forward to continuing our cherished friendship," it said.
Aniston was previously married to Brad Pitt from 2000 to 2005.
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