According to a report in The New York Times late on Monday, the co-founders have resigned from their positions and plan to leave the company in the coming weeks while the reason behind their move was still unknown.
Later, Systrom wrote in a blog post that they were planning on taking some time off to explore their curiosity and creativity.
"Building new things requires that we step back, understand what inspires us and match that with what the world needs; that's what we plan to do," said Systrom.
"We've grown from 13 people to over a thousand with offices around the world, all while building products used and loved by a community of over one billion. We're now ready for our next chapter," the blog post added.
The resignations came at a time when social media platforms including Facebook were facing intense scrutiny over the spread of fake news and sinister campaigns.
Instagram's meteoric rise continued after the acquisition, dwarfing the stagnant growth rates of Snapchat and Facebook.