Earlier Tuesday, Barclays analysts predicted WhatsApp would likely use more ads now that Koum has departed. Facebook bought WhatsApp for $19 billion in 2014.
"We've been told by many of our checks over the last few years that 'once Jan leaves, that's when the ads show up,'" the analysts said in a note.
While Koum gave no reason for his departure, The Washington Post reported that he was "worn down by the differences in approach" around a variety of issues, including ad-based revenue and data targeting.
Marcus said Koum simply decided he wanted to do something else right now and said it is "definitely not the case" that there was any internal dissent over data.
Facebook announced a redesign of Messenger at the developer conference on Tuesday.
"The goal was to simplify the system and to make sure that we could actually ensure that messaging was really at the center of everything that people wanted to do," Marcus told CNBC.
The big news from the conference was CEO Mark Zuckerberg's announcement that the social media giant is launching an opt-in dating feature. The news sent shares of online dating company Match plunging as much as 20 percent. Its parent company IAC also fell more than 10 percent.
— CNBC's Ingrid Angulo and Sara Salinas contributed to this report.