Chikungunya virus is a mosquito-borne virus that causes an acute febrile infection and severe arthralgia and is considered a re-emergent pathogen. During a study investigating arboviruses causing febrile infection in infants in Bata, Equatorial Guinea, the genome of this virus was amplified from blood samples during near two rainy seasons (2002-2003). In 2006, this virus was isolated from a traveler returning to Spain from Equatorial Guinea. These results show that chikungunya virus is present in this country and two lineages are circulating. Thus, this virus should be considered in the differential diagnosis of febrile syndromes in inhabitants and in travelers returning from this country.