Aeromexico Flight 668 was given clearance to land on Runway 28R at SFO Airport, but for unknown reasons, the pilots aligned the Boeing 737-800 with the runway next to it, 28L.
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At the same time, a Virgin America Airbus A320 was stopped on Runway 28L awaiting take-off to Kona, Hawaii, according to the FAA.
When Air Traffic Controllers noticed the mistake, they ordered the Aeromexico flight to abort the landing one mile from the airport. The pilots complied with the order and landed safely after making a second approach to SFO.
RELATED: Air Canada flight nearly lands on taxiway at San Francisco International Airport
The Virgin America flight departed without incident.
Air Traffic Control audio reviewed by ABC7 News indicated the pilots acknowledged the correct runway they were told to land on.
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The FAA said the Aeromexico pilots had been using their instrument landing system during the approach, which provides guidance to the pilots when landing in low visibility.
RELATED: NTSB investigating after Air Canada flight nearly lands on taxiway at SFO
The FAA plans to interview the pilots as part of their investigation.
Aeromexico says they are "investigating the events."
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Tuesday's incident follows a near mishap in July 2017 when an Air Canada flight from Toronto almost landed on a taxiway at SFO that was crowded with planes.
The FAA is investigating the Air Canada incident along with the National Transportation Safety Board.
Written and produced by Tim Jue