Cox and Zuckerberg appear to be divided over the company's new strategy announced last week that it would focus on privacy rather than connecting with the world at large.
Mr Daniels has watched over WhatsApp after the messaging service's founders, Jan Koum and Brian Acton, left the company over disagreements with Mr Zuckerberg past year. Cox is by most people seen as the second-highest-ranking person at Facebook after Zuckerberg. "He has played so many central roles at Facebook - starting as an engineer on our original News Feed, building our first HR teams and helping to define our mission and values, leading our product and design teams, running the Facebook app, and most recently overseeing the strategy for our family of apps", Zuckerberg wrote in his note, adding, " At the same time, as we embark on this new chapter, Chris Daniels has also chose to leave the company".
The news follows Zuckerberg's public post last week which outlined his intention to address the social media giant's privacy issues by shifting away from public posts and moving instead toward encrypted, ephemeral communications on its messaging apps.
Daniels, who had worked on Facebook initiatives in developing countries, had moved a year ago to WhatsApp, which is more popular than Facebook in many big emerging markets.
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Zuckerberg said he does not plan on hiring anyone to fill Chris Cox's chief product officer role.
Zuckerberg told Wired magazine on 6 March that "there will be a bunch of work inside the company to make sure that we have the right folks in the right roles" to bring Facebook's apps together and introduce more privacy features.
Cox, 36, was the former chief of staff to Zuckerberg on product development, and was responsible for Facebook's family of apps (Instagram, WhatsApp, Messenger and others).
The Facebook app will be overseen by Fidji Simo, who led the team for much of the past year while Cathcart was on paternity leave. In the meantime, Zuckerberg has asked all of the heads of each of the company's products to report directly to him. He also thanked both executives for all of their contributions and for helping make the company what it is today.