The $0.99 app, which allows users to take handwritten notes with a stylus or finger, has been downloaded more than 2 million times -- making it the fourth most-popular paid iPad app.
After the acquisition, Penultimate will remain an independent brand in the iTunes store and a paid app. The "one-man shop" behind the app, Ben Zotto, will join Evernote and help expand handwriting features in its products.
Evernote's first acquisition, image app Skitch, has also remained an independent app, but went from being paid to free when it was acquired. Evernote turned two other recent app acquisitions into Evernote Food and Instapaper-like Evernote Clearly, and a third will soon become an Evernote calendar app.
"Penultimate is the biggest acquisition in terms of revenue and users," Libin says. "It's the most mature company we have ever bought."
The acquisition comes just four days after Evernote announced a $70 million round of funding that valued the company at $1 billion.
While Evernote already has more than 1 million paying customers, Libin says the funding makes it easier for the company to take risks such as acquiring Penultimate before going public.