Koalas (Phascolarctos cinereus) are iconic Australian marsupials currently threatened by several processes. Infectious reproductive tract disease, caused by Chlamydia pecorum, and koala retrovirus infection are considered key drivers of population decline. The clinical sign of "wet bottom", a staining of the rump associated with urinary incontinence, is often linked to chlamydial urogenital tract infections. But, wet bottom has been recorded in koalas free of C. pecorum, suggesting other causative agents in those individuals. Current understanding of the bacterial community of the koala urogenital tract is limited. We used 16S rRNA diversity profiling to investigate the microbiome of the urogenital tract of ten female koalas. Five presented with wet bottom and five were clinically normal. We detected thirteen phyla across the ten samples, with Firmicutes occurring at the highest relative abundance. The order Lactobacillales comprised 70.3% of the reads from all samples. After normalising reads using DESeq2 and testing for significant differences, there were 25 operational taxonomic units more commonly found in one group over the other. This study provides an essential foundation for future investigations of both the normal microflora of the koala urogenital tract, and better understanding of the causes of koala urogenital tract disease.