Objective: The primary objective of this systematic review is to present current knowledge about the oncobiome of gynecological cancers. Methods: Our systematic review contains data about the oncobiome of uterine corpus cancer, ovarian cancer and cervical cancer. Articles about other gynecological cancers were excluded. Results: A total of 72 articles were included in our systematic review. In uterine corpus cancer, cervical cancer and ovarian cancer, representatives of bacteria, fungi, viruses and parasites can be found. The oncobiome of ovarian cancer is connected with the oncobiome of head and neck cancers. Our systematic review proved that the human papilloma virus is connected with ovarian and cervical cancer. Gut dysbiosis can be used as a marker of ovarian cancer. In cervical cancer, we found the difference between the microbiota of healthy patients and patients with cervical cancer. Methylobacter, Robignitomaculum, Klebsiella, Micromonospora and Microbispora have an impact on overall survival. The microbiome of uterine corpus cancer is more differentiated than in cancer-free samples. Chronic endometrial inflammation has an impact on endometrial microbiome. Discussion: Treatment of gynecological cancers is changing permanently. Chemotherapy, as a systematic treatment, is being left in the past. Modern methods of therapy are addressed to specific genes. In the past, researchers claimed that tumors are sterile. However, the newest research indicates that malignancies were found to have genetic fragments of pathogens, which can be used as vectors for medications or as markers for the detection of a specific malignancy. Three most common gynecological cancers are as follows: endometrial cancer, ovarian cancer and cervical cancer. Each of these has their specific microbiome, which can be used for oncological treatment. These discoveries create possibilities for new, efficient methods of treatment. This systematic review analyzes publications about the composition of the gynecological tumor microenvironment, correlation between microbiomes of different organs, the female reproductive tract and the microbiome of the female reproductive tract during malignancy. Moreover, we provide information on the influence of some pathogens on the treatment.