Zika virus strain 'imported from the Americas' to Africa
The WHO said it was concerned that the latest strain was spreading and was "on the doorstep of Africa".
It is currently circulating in Cape Verde, an archipelago off the north west coast of Africa.
Zika has been linked to neurological disorders including babies being born with small brains.
Dr Matshidiso Moeti, WHO Regional Director for Africa, said: "This information will help African countries to re-evaluate their level of risk and adapt and increase their levels of preparedness."
She said African countries should raise awareness among pregnant women of the complications with the Zika virus and encourage people to protect themselves against mosquito bites and sexual transmission.
But she said she would not recommend strict travel restrictions to try to stop the spread of the disease.
There have been more than 7,000 suspected cases of Zika in Cape Verde, with 180 pregnant women thought to have been infected. The WHO says three babies have been born brain damaged with microcephaly.
Until the virus was sequenced by scientists in Senegal, it was not certain if the outbreak in Cape Verde was caused by the African or Asian type, which has hit Brazil and other Latin American countries.
Tests show that this is the Asian strain - the same as the one blamed for birth abnormalities in Brazil.
There have been around 1,300 confirmed cases of microcephaly - babies born with small brains - in Brazil, with thousands more under investigation.
A UK researcher said the Zika virus has been circulating at a low level in African countries for more than 50 years, so some of the population may already be immune.
"It is likely that the South American, Caribbean and Polynesian populations had no prior immunity to the virus, so a high proportion of people who are bitten by infected mosquitos caught the disease," said Dr Anna Checkley, of the Hospital for Tropical Diseases, University College London Hospitals.