Penultimate, Cocoa Box’s popular handwriting app for iPad, is now part of the Evernote family. The deal was announced today via the Evernote blog.

Released soon after the original iPad came to market in 2010, Penultimate allows you to take notes, keep sketches, or share your next breakthrough idea using a simple interface. To date, it is the App Store’s No. 4 bestselling paid iPad app of all time.

As part of today’s announcement, Evernote made it clear that Penultimate will remain a “separate, elegant application.” Future updates, however, will bring “much-requested Evernote-y improvements including full search and synchronization.”

As Ben Zott0, creator of Penultimate states on the Penultimate site:

Importantly, Penultimate is not going away: it remains an independent application, and will continue to espouse the virtues of ease of use, elegance, and “that special something” that have kept you coming back. But I also think you’ll be thrilled, and even surprised, by how much more the app will be able to do for you as we work together to improve it and connect more profoundly with Evernote’s capabilities.

As part of the deal, Zotto will now head up Evernote’s future app development.

Take a look:

Evernote is an easy-to-use, free service that helps you organize “notes” to save your ideas across multiple platforms. Evernote lets you take notes, capture photos, create to-do lists, record voice reminders, and makes these notes completely searchable, whether you are at home, at work, or on the go.

Evernote (free) and Penultimate ($0.99) are available in the App Store.

Are you happy about today’s news or worried it could lead to Penultimate’s demise?