Australian scientists Tuesday hailed the discovery of two sea snake species feared to have become extinct years ago off the Western Australia coast.

The short-nose sea snake and the leaf-scaled sea snake had not been seen since disappearing from their only known habitat on Ashmore Reef in the Timor Sea more than 15 years ago, James Cook University researchers wrote in the Biological Conservation journal.

But they have since been "spotted alive and healthy" at Ningaloo Reef (short-nose sea snake) and Shark Bay (leaf-scaled sea snake), thousands of kilometres south.

"This discovery is really exciting, we get another chance to protect these two endemic Western Australian sea snake species," the study's lead author Blanche D'Anastasi said in a statement about the two species, listed by Australian authorities as critically endangered.

"But in order to succeed in protecting them, we will need to monitor populations as well as undertake research into understanding their biology and the threats they face."

The university said the short-nose sea snake was identified after a wildlife officer sent a photo of two of them to D'Anastasi in April 2013.

"What is even more exciting is that they were courting, suggesting that they are members of a breeding population," D'Anastasi added.

The scientists said it was a "real surprise" when they also discovered a "new and significant" population of the leaf-scaled sea snake in the seagrass beds of Shark Bay.

"The disappearance of sea snakes from Ashmore Reef could not be attributed to trawling and remains unexplained," said another researcher, Vimoksalehi Lukoschek.

Sea snakes are often vulnerable as by-catch by prawn trawlers.

"Clearly we need to identify the key threats to their survival in order to implement effective conservation strategies if we are going to protect these newly discovered coastal populations," Lukoschek added.