The honour has been bestowed on Charles, 63, the heir apparent to the British throne, in recognition of his charity work to protect their rainforest homes.
Hyloscirtus princecharlesi, or the Prince Charles stream tree frog, was first discovered by Dr. Luis A. Coloma in 2008 amongst specimens collected for a museum.
A subsequent expedition in the Cotacachi-Cayapas National Park, Ecuador, found limited numbers of the frogs after areas of the forest were cleared for agriculture, the BBC reported.
Two juvenile frogs are now being raised in captivity as part of the Amphibian Ark project in the hope they will breed and eventually boost populations in the wild.
Amphibian Ark, which works to ensure the survival of endangered frogs, newts and salamanders, decided to name the new species after Prince Charles.
A spokesman said: "It is endangered and needs to be protected in the wild, its rainforest habitat is under threat due to the impact of farming."
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"It's fairly unusual to name a new species after someone, but this is seen as something special in honour of the Prince," the spokesman added.
Charles met Dr Coloma yesterday at an environmental-themed workshop the Prince is hosting for young school children from across the country at Highgrove, his Gloucestershire home.