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Some intracellular symbionts of arthropods induce a variety of reproductive alterations in their hosts, and the alterations tend to spread easily within the host populations. A few cases involving the spread of alteration-inducing Wolbachia bacteria in natural populations with time have been reported, but the investigations on the increasing trend in counteracting the bacterial effect on hosts in natural populations (i.e., increased resistance in hosts against the alterations) have been limited. In the present study, the prevalence of an alteration, killing of male Hypolimnas bolina (L.) (Lepidoptera: Nymphalidae) butterflies by their inherited Wolbachia strain in the wild in Japan, was surveyed over a continuous 50-year period, which is far longer than ever before analyzed in studies of dynamics between reproductive alteration-inducing symbionts and their host arthropods. Thus, the results in this study provide the first instance of a long-term trend involving a change in reproductive alteration; and it strongly suggests a change in the opposite direction (i.e., suppression of male-killing) in natural populations. This change in the current combination of the Wolbachia and butterflies appears to be dependent upon the host taxon (race).