Maternally inherited
Wolbachia
endosymbionts manipulate arthropod reproduction in various ways. In the butterfly
Eurema mandarina
, a cytoplasmic incompatibility-inducing
Wolbachia
strain
w
CI and the associated mtDNA haplotypes are known to originate from the sister species
Eurema hecabe
, which offered a good case study for microbe-mediated hybrid introgression. Besides
w
CI, some females with the Z0 karyotype harbour a distinct
Wolbachia
strain
w
Fem, which causes all-female production by meiotic drive and feminization. We report that a considerable proportion of
E. mandarina
females (65.7%) were infected with both
w
CI and
w
Fem (CF) on Tanegashima Island. While females singly infected with
w
CI (C) produced offspring at a 1 : 1 sex ratio, CF females produced only females. Although Z-linked sequence polymorphism showed no signs of divergence between C and CF females, mtDNA split into two discrete clades; one consisted of C females and the other CF females, both of which formed a clade with
E. hecabe
but not with uninfected
E. mandarina
. This suggests that CF matrilines also, but independently, experienced a selective sweep after hybrid introgression from
E. hecabe
. Distinct evolutionary forces were suggested to have caused C and CF matrilines to diverge, which would be irreversible because of the particular phenotype of
w
Fem.