By Reed Albergotti and Greg Bensinger 

David Marcus, president of eBay Inc.'s PayPal payments subsidiary, is leaving to become Facebook Inc.'s vice president of messaging products.

At Facebook, Mr. Marcus will run Facebook Messenger, a standalone app as well as a feature in Facebook's desktop platform. But he won't oversee WhatsApp, the mobile-messaging service Facebook agreed to buy for $19 billion in February, a Facebook spokeswoman said.

The high-profile hire is the latest example of Facebook's push into mobile messaging, an increasingly important part of its plan to connect the world through its platform.

Facebook Messenger has a fraction of the users that WhatsApp does. In many countries it trails far behind other popular services such as Line and WeChat. Facebook said 12 billion messages are sent through its messenger service every day, and around 200 million people use the service every month. By contrast, WhatsApp has more than 500 million monthly users.

In April, Facebook began forcing mobile users to download Messenger to send and read messages from other users. Facebook previously had included that function in its main mobile app.

Mr. Marcus and other senior eBay managers spent much of the early part of the year defending PayPal from activist investor Carl Icahn, who was pressing eBay to spin off the payments unit. Mr. Icahn ultimately relented, agreeing to insider status at the company.

An eBay spokeswoman said Mr. Icahn played no role in Mr. Marcus's departure.

It isn't clear why Facebook is putting so many resources in its own messaging service when it paid such a steep price to acquire another one. Last week, WhatsApp co-founder Brian Acton called the Facebook Messenger "separate but equal" from WhatsApp, but didn't elaborate.

Facebook founder and Chief Executive Mark Zuckerberg has said the apps are used differently. Facebook Messenger is used by people to stay in touch with friends and relatives, who may not expect an immediate response. WhatsApp is used for more-instant communication, as a replacement for text-messaging conversations.

On Monday, Facebook accidentally released a version of Slingshot, an app that works in a similar way to the disappearing-message app Snapchat. According to the company spokeswoman, Facebook's Creative Labs division is working on the app and hopes to release it officially soon. The spokeswoman said Mr. Marcus will have no involvement with Slingshot.

In explaining his jump to Facebook, Mr. Marcus said on his Facebook page that Mr. Zuckerberg had shared his "compelling vision" for mobile messaging, which "won me over."

The eBay spokeswoman said Mr. Marcus decided to leave on his own. She said the move was effective at the end of June, after which eBay CEO John Donahoe would lead PayPal on an interim basis. EBay said it would look inside and outside the company for a successor.

In a statement, Mr. Donahoe said Mr. Marcus had helped with "reinvigorating product design and innovation" at PayPal.

Mr. Marcus said he felt comfortable leaving PayPal after two years at the helm because the company was in good shape. "PayPal is on track to achieve the greatness it deserves in the years to come," he said.

Write to Reed Albergotti at reed.albergotti@wsj.com and Greg Bensinger at greg.bensinger@wsj.com

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