Confirming the news on their individual Instagram accounts, Katya and Neil shared an image of a statement with a heart emoji as the caption.
The statement explained the couple have made a “mutual decision to separate” after 11 years together.
The couple, who are both professional dancers on the BBC show, celebrated their sixth anniversary earlier this month.
The statement, posted on both their social media pages, read: “Hi everyone, as our fans and loyal supporters you are really important to us and so we wanted to let you know some news.”
The statement then announced the couple’s decision to split and explained: “We will always love each other, just in a different way as friends.
Despite the split, the couple say they “will always have love for each other” and plan to “keep working and dancing together”.
They ended their statement by saying: “We wish one another every happiness and we will remain the best of friends.
“We are really looking forward to getting back to the ballroom and can’t wait to keep dancing.”
It comes ten months after Katya was pictured kissing her celebrity dance partner Seann Walsh, 33, on a night out.
A spokesperson for Katya and Neil denied the kiss was linked to the couple’s split and said: “It would be incorrect and unfair to attribute their separation to one isolated incident.
“Many people make such a decision to separate when they realise that their relationship has become more of a friendship. They remain the very best of friends and will continue to dance together.”
Seann and Katya made a public apology on Strictly’s spin off show, It Takes Two, as Seann said: “Obviously I’m sorry for the hurt that I have caused. We were getting along well, we were having fun, we had a couple of drinks and made a huge mistake, and I deeply regret it.”
Katya also apologised in October for her actions, adding: “I can’t apologise enough to everyone who it hurt and involved.
“But, the main thing, me and Neil are absolutely fine and that’s what matters to me the most right now and focusing on my job and doing it as professionally I can.”
Katya’s husband Neil forgave his wife for the kiss and the pair later headed off on a make-or-break holiday at the beginning of the year.
In December, Neil opened up about his marriage to Katya for the first time after the kissing scandal.
In an Instagram question and answer session, one fan asked: “Are you back with Katya?”
Making a rare comment about their marriage, Neil wrote at the time: “I’ve never been away from Katya,” and shared a photo of the pair looking close.
Neil and Katya met over a decade ago at a dance competition in Blackpool. During the tournament, the couple were paired up by a dance coach after Katya found herself without a partner.
The couple were inseparable both on and off the dance floor after meeting and married in 2013.