(Read about another mysterious ray, Asia's giant river stingray.)
The species discovery was the unexpected result of five years of hard work and a bit of good fortune, Marshall said.
"As luck would have it, it looks like here in Mozambique is the only [known] location where we see both species interacting on the same reef," said Marshall, whose effort was funded by the Switzerland-based Save Our Seas Foundation.
Though much of Marshall's time was spent underwater, she also logged long hours collecting data around the world in a search for proof that the species were distinct.
To build her case she pursued evidence from DNA labs and Indonesian fishing villages, where the migrating species is still commonly caught.
Rachel Graham of the Wildlife Conservation Society in Punta Gorda, Belize, was impressed by Marshall's work, one of the longest-running manta studies ever conducted.
"We were just incredibly excited about this," she said. "The work was very in-depth and I think [for the most part] the group was convinced."
The new species discovery will add to challenges for those seeking to protect the vulnerable, slow-to-reproduce rays.
(Related: "Photo: First Giant Manta Ray Born in Captivity Dies" [June 18, 2007].)
The smaller manta species is at risk because of their limited range.
"If someone comes into a coastline or island group and starts up a fishery, you could wipe out that population in a year or two," University of Queensland's Marshall said.
"That would [threaten] regional extinction like what may [be happening] in the Gulf of California."
The migratory mantas provide their own challenges, she added. They respect no borders, so protection efforts must involve a complicated cooperation between many nations and groups.
"Both species face independent issues in terms of conservation management," Marshall said. "We have to understand the threats to each."
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