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The composition of host-associated microbial communities may correlate with the overall status of the host, including physiology and fitness. New bi-directional hypotheses suggest that sexual behaviors can shape, and be shaped by reproductive microbiomes, which may be particularly important for species with mating systems that feature strong sexual selection. These dynamics have been particularly understudied in female animals. Using 16S rRNA sequencing, we compared the cloacal microbiome of females and males from two socially polyandrous bird species that vary in the strength of sexual selection, Jacana spinosa (Northern Jacana) and J. jacana (Wattled Jacana). We hypothesized that the strength of sexual selection would shape cloacal microbial diversity, such that the more polyandrous J. spinosa would have a more diverse microbiome, and that microbiomes would be more diverse in females than in males. If the reproductive microbiome is indicative of competitive status, we also hypothesized that cloacal microbial diversity would be associated with competitive traits, including plasma testosterone levels, body mass, or weaponry. We found no differences in microbial alpha diversity between species or sexes, but we did find that microbial beta diversity significantly differed between species. We also found a positive relationship between microbial alpha diversity and testosterone in female J. spinosa. Future experiments are needed to explore the potential drivers of correlations between the cloacal microbiome and competitive phenotypes in socially polyandrous jacanas.