Fishing guides and rafting operators who run businesses along the river yesterday said the move could be catastrophic to the area's sizable outdoor industry, which depends heavily on the busy summer season.
The closure could extend for months if river conditions don't improve and fish keep dying, according to officials from Montana Fish, Wildlife and Parks. It includes hundreds of miles of waterways that feed into the Yellowstone, including the Boulder, Shields and Stillwater rivers.
"This kill is unprecedented in magnitude. We haven't seen something like this in Montana," Fish, Wildlife and Parks spokeswoman Andrea Jones said.
By yesterday, roughly 4,000 dead fish had been counted, but the total number is estimated to be in the tens of thousands, including fish that sank to the bottom, officials said.
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Most have been mountain whitefish, a native game species, but reports also emerged that the die-off has affected some rainbow trout and Yellowstone cutthroat trout species crucial to the area's fishing industry.
The closure on the Montana portion of the river aims to stop the spread of the parasite, which causes fish to contract a fatal kidney disease, and to protect the fishery and the outdoor economy it sustains, officials said.
The disease was previously documented just twice in the state over the past 20 years but more recent outbreaks have occurred in Washington, Oregon and Idaho. Officials said it does not pose a health risk to people.