The hunt, New Jersey's first since 2005, is part of the state Department of Environmental Protection's bear management policy.
Wildlife officials have said the hunt, which ended at dusk on Saturday, was needed to reduce a black bear population now thought to number about 3,400.
But opponents contend the policy was improperly developed.
Two animal rights groups - Animal Protection League and Bear Education and Resource Group - tried unsuccessfully to stop the hunt before it started.
But an appeals court refused to halt the hunt on Dec. 3, and the following day a judge acting on a petition to the state Supreme Court refused to grant an emergency stay. The lawsuit, which challenges the state's bear management policy as improper, is continuing.
A similar challenge succeeded in 2007 and no hunt was held. An appeals panel found flaws with the management policy and ruled that the 2005 hunt should not have taken place.
Some 6,680 bear hunting permits were issued for this year's hunt, with each hunter entitled to one bear regardless of age or gender. The DEP has estimated that as many as 700 bears will be killed overall.