HMS Enterprise created a series of spectacular 3D images using a multi-beam echo sounder.
The canyon was found during a nine-month mission to improve understanding of the waters east of Suez, the 'Independent' reported.
"These features could be the result of ancient rivers scouring through the rock strata before the Red Sea flooded millennia ago," Derek Rae, commanding officer of HMS Enterprise, said.
"Some may be far younger and still in the process of being created by underwater currents driven by the winds and tidal streams as they flow through this area of the Red Sea, carving their way through the soft sediment and being diverted by harder bed rock.
A canyon is a deep gorge, typically one with a river flowing through it, as found in North America.