Cox's bombshell comes just one week after Zuckerberg announced that Facebook would become a "privacy-focused" company. Zuckerberg wrote that Cox considered leaving years ago to pursue new projects, but he chose to stay in 2016, around the time Facebook began taking heat for acting as a conduit for misinformation and Russian election interference.
Will Cathcart was announced as the new lead on WhatsApp, while Zuckerberg, apparently consolidating power as he prepares to merge the apps in some way or another, states he does "not plan on immediately appointing anyone to fill Chris's role in the near term".
Cox made his announcement in on his Facebook page, saying he was leaving "with great sadness" after 13 years.
Two of Facebook's top executives are leaving the social network - a week after its boss Mark Zuckerberg announced a big strategic pivot toward private messaging. In May, Cox was put in charge of Facebook's "family of apps", including Instagram, Messenger, WhatsApp and Facebook itself - which together have over 2.7 billion users worldwide.
"This is an important change as we begin the next chapter of our work building the privacy-focused social foundation of the future", Facebook CEO Mark Zuckerberg wrote in a statement. Daniels worked for Facebook for eight years, and was promoted to oversee WhatsApp last May.
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The departures of Cox and Daniels come a day after a technical issue that limited use of Facebook and Instagram for most of Wednesday.
"This will be a big project and we will need leaders who are excited to see the new direction through", he wrote. Longtime Facebook executive Will Cathcart will take over Daniels' job running WhatsApp. Meanwhile, Javier Olivan will lead the effort to better integrate the Facebook apps.
Numerous changes Zuckerberg outlined involve duplicating some of WhatsApp's features in Facebook's other messaging apps.
While Zuckerberg also said that Cox had spoken before about his desire to leave the company, that his departure is tied directly to Facebook's so-called privacy pivot, is significant.
Facebook's social network and Instagram photo app won't change, and will remain available for sharing places, adventures and minutiae with a broader audience.