The objective of this study was to systematically review the literature on the human microbiome in association with endometriosis. PubMed/Medline, Cochrane, and Embase databases were searched for literature published from 1986 to August 2021. All human studies that assessed the microbiome using 16S rRNA sequencing or by Shotgun Sequence in women with endometriosis were included. Two reviewers independently abstracted data from the selected articles into tables. To assess the quality of included studies, NIH Study Quality Assessment Tools were utilized. This review included 12 case-control studies. Included studies compared the microbiome from various anatomical sources (fecal, vaginal, cervical, peritoneal, endometrial, intra-lesional) between patients with endometriosis and a heterogeneous set of control patients. Study quality ranged from poor to good, with 8 of 12 studies rated fair. Multiple studies reported on a different distribution of bacteria among women with endometriosis across anatomical sites, but results were highly heterogeneous. Pseudomonas was overrepresented in peritoneal fluid among women with endometriosis across multiple studies, but was also observed increased in vaginal, endometrial, and intra-lesional samples. Among bacteria noted across different anatomical samples, Gardnerella was increased in cervical but decreased in endometrial, fecal, and vaginal samples of patients with endometriosis, while Atopium was decreased in vaginal and cervical samples from patients with endometriosis. Sphingobium was increased in vagina, endometrium, and peritoneal fluid from patients with endometriosis. Streptococcus was increased peritoneal, endometrial, and cervical samples from women with endometriosis. Microbiomal comparisons stratified by endometriosis stage or site of endometriosis involvement were limited and highly heterogeneous.