The She's All That star revealed the news on Thursday in a heartfelt statement posted to Instagram, which she captioned simply with a heart emoji.
"With deep gratitude for every year we have spent together and the thousands of beautiful memories shared, we have mutually decided to separate as a couple," Cook wrote. "This decision isn't one we have come to easily or lightly."
"We love and respect each other as parents, people and artists and look forward to maintaining the best parts of our relationship for many years to come," added Cook, who shares two children with Gilles -- 5-year-old daughter Charlotte and 4-year-old son Theodore.
"Your discretion in this matter is kindly requested for the sake of our children during this time of transition," she concluded. "Thank you to those of you who are already aware; for your tremendous compassion and understanding. Lots of love, Rachael and Daniel."
The pair began dating in 2001 and tied the knot in August 2004.
ET spoke with Gillies in April 2017, where the star had nothing but love and positivity about his marriage to his "beautiful" wife and reflected on how enamored he's been with her since the start of their relationship.
"This is going to sound like the creepiest thing of all time, but when I was first married her… I remember just watching her sleep and thinking that is the most beautiful person and I would just watch her for a while," Gillies shared.
He also marveled over their children, sharing with a smile, "It's amazing to see when our kids have inherited some of her physical characteristics."
Check out the video below for more on the couple and their family.