"This discovery is really exciting, we get another chance to protect these two endemic Western Australian sea snake species," said study lead author Blanche D'Anastasi from the James Cook University in Australia.
"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," D'Anastasi said.
It is the first time the snakes have been spotted alive and healthy since disappearing from their only known habitat on Ashmore Reef in the Timor Sea more than fifteen years ago.
"We were blown away, these potentially extinct snakes were there in plain sight, living on one of Australia's natural icons, Ningaloo Reef," said D'Anastasi.
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"What is even more exciting is that they were courting, suggesting that they are members of a breeding population," she said.
The researchers also made another unexpected discovery, uncovering a significant population of the rare leaf scaled sea snake in the lush seagrass beds of Shark Bay.
"We had thought that this species of sea snake was only found on tropical coral reefs. Finding them in seagrass beds at Shark Bay was a real surprise," said D'Anastasi.
Both leaf scaled and short nosed sea snakes are listed as Critically Endangered under Australia's threatened species legislation, which means they have special protection.
Sea snake numbers have been declining in several marine parks, and scientists are at a loss to explain why.
"Many of the snakes in this study were collected from prawn trawl by-catch surveys, indicating that these species are vulnerable to trawling," said Vimoksalehi Lukoschek from the Centre of Excellence for Coral Reef Studies.
"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 said.