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Horizontal transmission between distantly related species has been used to explain how
Wolbachia
infect multiple species at astonishing rates despite the selection for resistance. Recently, a terrestrial isopod species was found to be infected by an unusual strain of supergroup F
Wolbachia
. However, only
Wolbachia
of supergroup B is typically found in isopods. One possibility is that these isopods acquired the infection because of their recurrent contact with termites—a group with strong evidence of infection by supergroup F
Wolbachia
. Thus, our goals were: (1) check if the infection was an isolated case in isopods, or if it revealed a broader pattern; (2) search for
Wolbachia
infection in the termites within Brazil; and (3) look for evidence consistent with horizontal transmission between isopods and termites. We collected
Neotroponiscus
terrestrial isopods and termites along the Brazilian coastal Atlantic forest. We sequenced and identified the
Wolbachia
strains found in these groups using
coxA
,
dnaA
, and
fpbA
genes. We constructed phylogenies for both bacteria and host taxa and tested for coevolution. We found the supergroup F
Wolbachia
in other species and populations of
Neotroponiscus
, and also in
Nasutitermes
and
Procornitermes
termites. The phylogenies showed that, despite the phylogenetic distance between isopods and termites, the
Wolbachia
strains clustered together. Furthermore, cophylogenetic analyses showed significant jumps of
Wolbachia
between terrestrial isopods and termites. Thus, our study suggests that the horizontal transmission of supergroup F
Wolbachia
between termites and terrestrial isopods is likely. Our study also helps understanding the success and worldwide distribution of this symbiont.