Microbes interfere with the olfactory communication of animals by degrading chemical signals or by adding volatile metabolites. We report on the composition and diversity of the microflora in a sexually selected scent organ, the wing sacs of Saccopteryx bilineata, which are used by males for courting females. Wing sacs lack any glandular tissues. Instead, males clean and refill their wing sacs each day with genital and gular secretions. Females have only a nonfunctional rudiment of this organ. We isolated a total of 40 microbial species with only a moderate overlap in species composition between the sexes. The estimated microbial diversity was significantly lower in males than in females, with a minimum of 52.5 microbial species ± 5.0 SD in wing sac rudiments of females and 40.3 ± 4.2 SD in wing sacs of males (jackknife estimates). Males carried on average only 2 out of 40 possible microbial species in their wing sacs. Thus, individual scent profiles of males could originate from individual microflora. The daily routine of wing sac cleaning and refilling has possibly evolved to control microbial scent degradation, to support an individual microflora involved via volatile metabolites in mate choice, or both. Microbes may play a more prominent role in the evolution of morphological structures and behavioral adaptations than previously envisaged.