The Bachelor host announced the end of the couple's relationship on Thursday "after much heartfelt consideration".
"Though we have made this incredibly difficult decision to separate, our love and mutual respect remain, and we look forward to sharing in the lives of our wonderful children," they said in a statement.
Chris and Gwen are parents to two sons, 9-year-old Joshua and 7-year-old Taylor.
Harrison will host the new season of The Bachelorette, premiering May 14 on ABC.
It was recently reported that casting for the 17th season of The Bachelor had begun.