During the last decade, the endosymbiont bacterium
Wolbachia
has emerged as a biological tool for vector disease control. However, for long time, it was believed that
Wolbachia
was absent in natural populations of
Anopheles
. The recent discovery that species within the
Anopheles gambiae
complex host
Wolbachia
in natural conditions has opened new opportunities for malaria control research in Africa. Here, we investigated the prevalence and diversity of
Wolbachia
infection in 25 African
Anopheles
species in Gabon (Central Africa). Our results revealed the presence of
Wolbachia
in 16 of these species, including the major malaria vectors in this area. The infection prevalence varied greatly among species, confirming that sample size is a key factor to detect the infection. Moreover, our sequencing and phylogenetic analyses showed the important diversity of
Wolbachia
strains that infect
Anopheles
. Co‐evolutionary analysis unveiled patterns of
Wolbachia
transmission within some
Anopheles
species, suggesting that past independent acquisition events were followed by co‐cladogenesis. The large diversity of
Wolbachia
strains that infect natural populations of
Anopheles
offers a promising opportunity to select suitable phenotypes for suppressing
Plasmodium
transmission and/or manipulating
Anopheles
reproduction, which in turn could be used to reduce the malaria burden in Africa.