Gardnerella vaginalis is a hallmark of vaginal dysbiosis, but it is found in the microbiomes of women with and without vaginal symptoms and those who do not have microbiologically defined dysbiosis. G. vaginalis encompasses diverse taxa differing in attributes that are potentially important for virulence, and there is evidence that clades or subgroups within the species are differentially associated with clinical outcomes. The G. vaginalis species description was recently emended, and three new species within the genus were defined (G. leopoldii, G. swidsinskii, and G. piotii). 16S rRNA sequences for the four Gardnerella species are all >98.5% identical, and no signature sequences differentiate them. We demonstrated that Gardnerella species can be resolved using partial chaperonin 60 (cpn60) sequences, with pairwise percent identities of 87.1 to 97.8% among the type strains. Pairwise cooccurrence patterns of Gardnerella spp. in the vaginal microbiomes of 413 reproductive aged Canadian women were investigated, and several significant cooccurrences of species were identified. Abundance of G. vaginalis and G. swidsinskii was associated with vaginal symptoms of abnormal odor and discharge. cpn60 barcode sequencing can provide a rapid assessment of the relative abundance of Gardnerella spp. in microbiome samples, providing a powerful method of elucidating associations between these diverse organisms and clinical outcomes. Researchers should consider using cpn60 instead of 16S RNA for better resolution of these important organisms.