"Thank you for everything you've done for Twitter Adam! I have learned so much from you, and appreciate everything you stand for," co-founder and CEO Jack Dorsey replied.
Messinger has been working with Twitter for five years and became the CTO in March 2013. As chief technology officer, Messinger was responsible for engineering, product development, and design.
Josh McFarland, vice president of product at Twitter, will also leave the company early next year, to become a partner at top-tier Silicon Valley venture firm Greylock Partners. The company hired Keith Coleman, who rarely tweets, as vice president of product earlier this month.
Twitter's leadership ranks have been roiled by turnover, with product guru Dorsey back at the helm just over a year, while also juggling duties at Square.
Adam Bain stepped down as chief operating officer last month. The company replaced Bain with Anthony Noto, leaving Twitter in search of a chief financial officer. Twitter has also lost leaders from business development, media and commerce, media partnerships, human resources, and engineering this year.
Employee morale at Twitter has reportedly struggled this year, with some employees not showing up for work as of October,The New York Times reported. Twitter said in October it would lay off 9 percent of its employees and shut down video app Vine to keep its costs down.
As Twitter's advertising revenue and user growth have failed to keep pace with companies like Facebook , it has been widely speculated that the company might sell itself. Shares have fallen more than 22 percent in a rollercoaster trading year, as no clear buyers emerged for the social media property.
While Twitter is used with much influence by powerful people like president-elect Donald Trump, Twitter has looked to revive its product with live streaming events like presidential debates and NFL games.
— Reuters contributed to this report.