Route 5 is closed in both directions near the I-90 West in Corfu because a tractor trailer ran off the road.
The incident happened around 4:30 Friday morning.
New York State Police said the vehicle went off the Thruway, down an embankment and came to rest on Route 5.
A female passenger in the tractor trailer, the driver's wife, was flown to a Buffalo hospital.
The male driver was taken there by ambulance.
Genesee County's Sheriff's deputies said both are expected to survive.
There were two dogs in the truck at the time. One was found by first responders and taken to a veterinarian, but the other hasn't been found.
They say there's no word when Route 5 will reopen.
"As you can see, the truck is not gonna upright very easily,” said Jamie Waff, interim chief of the Pembroke Fire Department. “There’s multiple pieces and frame’s bent so it’s gonna be a while."
Waff said DEC crews were called to clean out 100 gallons of diesel fuel that leaked from the tractor trailer into a drainage pit.