[Updated at 1:07 pm with comments from Paper.]

Paper has been around for nearly 2,000 years, but now a battle for its name is brewing in the digital world.

Facebook launched a new mobile news app called “Paper” last week. 

However Paper is already the name of another popular app out there — the first and flagship app of a startup called FiftyThree — and CEO Georg Petschnigg would prefer if Facebook chose a different name.

“We reached out to Facebook about the confusion their app was creating, and they apologized for not contacting us sooner. But an earnest apology should come with a remedy,” Petschnigg said in a blog post. “There’s a simple fix here. We think Facebook can apply the same degree of thought they put into the app into building a brand name of their own. An app about stories shouldn’t start with someone else’s story. Facebook should stop using our brand name.”

Paper takes tools that stimulate creativity, such as pencils, pens, markets, and paints, and turns them into digital versions. It recently passed 100 million pages created and Apple designated it the 2012 iPad app of the year.

Then Facebook came along and created “broad-based confusion.”

Facebook’s Paper is the first product to emerge out of Creative Labs. The department was formed after Facebook acquired Push Pop Press in 2011, a design-focused iPad publisher led by Apple designer Mike Matas.

The app takes stories from your News Feed and organizes them into themes and interest categories. The editorial team behind Paper will also surface trending topics and important news stories of the day.

Facebook made the announcement about Paper on Thursday, and Petschnigg said he learned about it along with everybody else.

“I got back from the gym that morning and my inbox was full of people asking questions — confused customers, congratulations from friends who thought we got acquired, our investors wondering if we made a deal,” he said in an interview. “Walking alongside a giant is tricky when you are a small startup, that became very apparent over the next few days.”

Facebook has had some mobile missteps over the years, but Paper is well-conceived, beautifully designed, and has received rave reviews from publications, including Forbes and The Verge.

One of the reasons Facebook’s Paper has generated such excitement is it shows the social networking giant still has the ability to surprise and delight its users and innovate like a startup. However Petschnigg said that by using the name Paper, Facebook is essentially stomping over the little guy.

“The ideal outcome is that Facebook changes the name,” Petschnigg said. “It doesn’t matter what size your company is, you can’t use another company’s trademark. I strongly believe even a company the size of Facebook can act in human way and do the right thing.”

In another interesting twist, an iOS app developer called MiSoft claims it had an app called Paper, before Paper, before Paper.