"We are living separately and we are much happier this way," the pair told E! News in a joint statement.
"But we will always have much love and respect for each other Even though we are separated, we will always remain best friends and, as always, our family will remain our number one priority."
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A source close to the family told People, "There's actually no real drama. Bruce moved to Malibu in June and they liked that arrangement better. They just acknowledged they are separated."
The couple, who have two daughters together — Kendall, 17 and 16-year-old Kylie — and four children each from previous relationships, have faced numerous split rumours in recent months.
According to US Weekly, they kept their separation a secret for an entire year and will not divorce because they have no prenuptial agreement in place.
Their breakup is the latest marital problem for the famous family.
Kris's daughter Khloé Kardashian and her husband Lamar Odom are struggling with their own relationship. And earlier this year, Kim Kardashian finalised her divorce from Kris Humphries — 12 days before the arrival of her daughter North with partner Kanye West.
Kris, 57, and Bruce, 63, were married in April 1991, one month after the matriarch got divorced from her husband Robert Kardashian.
Bruce has been like a second father to the Kardashian children even since their father passed away in 2003.