After bouncing back from near-extermination last century, grizzlies were declared recovered in 2007, when they were stripped of their threatened status under the Endangered Species Act.
But in a 46-page ruling delivered Monday, U.S. District Judge Donald Molloy sided with environmental groups who argued the bruins remain at risk.
Among other factors, he cited a decline in whitebark pine trees -- a key food source for many bears that has been disrupted by climate change, forest fires and other factors.
Government researchers have made similar links, but that research was downplayed by the U.S. Fish and Wildlife Service in its 2007 decision.
"There is a disconnect between the studies the agency relies on here and its conclusions," Molloy wrote in his ruling. "These studies still state that there is a connection between whitebark pine and grizzly survival."
The greater Yellowstone area of Montana, Idaho and Wyoming has the second-largest grizzly bear population in the lower 48 states. Four other populations with a combined estimated population of 900 animals have never lost their threatened status.
Grizzlies are omnivores, meaning they eat both plants and animals. In the Yellowstone area, the bears rely heavily on nuts from the cones of the whitebark pine, a high-elevation tree that has suffered a dramatic decline in recent years as warmer temperatures let pine-killing beetles flourish.
A Fish and Wildlife spokesman declined to comment directly on Molloy's ruling, saying agency staff needed to review it.
"We're going to take some time with this rule because it's so significant," spokesman Matt Kales said. "This is obviously a pretty big policy matter for us. Our first and foremost concern remains with the status of the bear."
Environmentalists welcomed the ruling and said it underscored the need for government agencies to pay more heed to the potential damage climate change can cause for at-risk animal and plant species.
"The decline of the whitebark pine is one more wake-up call that we urgently need to address the cause of many species' impending extinctions," said Michael Robinson with the Center for Biological Diversity, a plaintiff in a separate federal lawsuit over grizzlies in Idaho that remains pending.
In his ruling, Molloy also said state and federal conservation plans meant to protect Yellowstone-area grizzlies into the future were inadequate.