The Swiss-based conservation group said on Friday it was "deeply concerned" about a new census showing the hippo population in the Virunga National Park had been slashed by 95% to around 1300 from 29,000 less than 30 years ago.
"WWF is concerned that unless trade is closely controlled and poaching is stopped, hippos will be threatened with extinction," said Susan Liebermann, Director of the World Wide Fund for Nature's International Species Programme.
And it is not only the hippos that are under threat.
Marc Languy of WWF's eastern Africa regional programme said, "Hippos are extremely important in maintaining the ecological balance in rivers and lakes and nearby grasslands.
"Hippos' dung provides essential basic elements for the food chain, particularly for fish.
"The loss of more than 27,000 hippos in the past few decades is a double blow; fish catches have dwindled and the freshwater ecosystems are losing hundreds of tons of nutrients every day.
"Lake Edward supports over 20,000 people living around the park who depend on fish for their livelihood."
The park, a world heritage site on the DRC's eastern border, was at the heart of inter-factional fighting which until this year prevented both the WWF and the Congolese Institute for the Conservation of Nature (ICCN), which carried out the census, from working in significant areas, WWF said.
But the group expressed hope that a peace deal signed in April to end four years of bloodshed in Africa's third biggest country would allow the government to put in place proper planning and management of the country's natural resources.
WWF urged DRC authorities to work with conservation groups to protect the rare mountain gorilla also found in the park, and halt the slaughter of hippos "in shocking numbers" as demand for their teeth increased in the illegal ivory trade.