Conflicts between individuals of the same species are common in nature and are mostly resolved with limited aggression. Several theoretical studies, such as the Hawk-Dove (HD) game model, investigate the evolution of limited aggression expressed during conflicts between individuals. These studies mainly focus on the individuals involved in the conflict and their genes. Recently accumulating evidence indicates that microbes are associated with diverse functions of their host and can affect host behavior. Here we extend the classic HD game model to include both the hosts and their microbes, examining how natural selection acts on the microbes. We find that nonaggressive host behavior is more likely to evolve and spread in a population when induced by the microbes residing in the host, compared to nonaggressive behavior induced by host genes. Horizontal transmission allows microbes to colonize new hosts, making their success dependent on the fitness of both the host and its opponent. Therefore, selection on the microbes favors reduced host aggressiveness under wider conditions compared to selection acting on genes alone. Our results suggest that microbes may help explain the ubiquity of nonviolent conflict resolution. Consequently, factors that alter the microbial composition within hosts may affect the aggressiveness level in host populations.