Two species of sea snakes, both listed as critically endangered and previously feared to be extinct, have been discovered living off the West Australian coast.

Researchers said the discovery of the short-nosed sea snake on Ningaloo Reef and the rare leaf-scaled sea snake at Shark Bay were the first time they had been spotted alive and healthy in 15 years.

Their only previous known habitat was nearly 2,000 kilometres away on Ashmore Reef in the Timor Sea, but they disappeared from there, a phenomenon scientists were at a loss to explain.

Scientists at Queensland's James Cook University (JCU) made the discovery, working in collaboration with WA's Department of Fisheries and Department of Parks and Wildlife.

JCU PhD student Blanche D'Anastasi said she was stunned by the discoveries.

"We were absolutely blown away," she said.

"When the snakes went extinct at Ashmore Reef there was global alarm ... the last thing we expected to find was the two missing sea snakes and there they were, in plain sight."

Ms D'Anastasi said it was particularly encouraging that the discovery of the short-nosed sea snake showed the two snakes in the midst of their courting process.

"Those two sea snakes were obviously in courting mode and hopefully getting ready to make babies and create future generations of short-nosed sea snakes," she said.

Ms D'Anastasi said the discoveries meant there was a significant need for further research and examination of the areas in which they were found.

"We discovered these snakes well out of their range and in entirely new habitats," she said.