Lawyer Chagay Netzer said the "Kippa Man" store was violating the intellectual property rights of both companies. DC Comics and Marvel are each demanding 25,500 U.S. dollars in damages and expect the store to stop selling the kippas.
The popular downtown store draws hordes of tourists with its colorful skullcaps, many featuring cartoon characters or sports insignia.
The separate lawsuits were served last week. The shop's owner declined to comment.
The Associated Press obtained copies of the lawsuits listing DC and Marvel as plaintiffs on Wednesday.