Purpose Recent advances in molecular biology technology have allowed identification of microbial communities in the urinary tract, and urinary microbiome is associated with various urological diseases. In this study, we aimed to characterize the urinary microbiome of genitourinary malignancies. Materials and Methods Metagenomic analysis of urinary DNA was performed in 85 patients including 30 with bladder cancer (BC), 27 with prostate cancer (PC), 12 with renal cancer (RC), and 16 with non-cancer (NC). 16S rRNA gene sequencing was conducted after amplification of the V3–V4 region. Results PC and RC had significantly lower Shannon index than BC, and beta diversity showed significantly different microbiome composition between four groups. We identified six genera of Cutibacterium , Peptoniphilus , Sphingomonas , Staphylococcus , Micrococcus , and Moraxella , which showed significantly different abundance between the four groups. When each of the malignancies were compared to NC at the species level, Micrococcus sp. was significantly increased in BC. We also identified 12 and five species with increased populations in PC and RC, respectively. Of these, Cutibacterium acnes , Cutibacterium granulosum , Peptoniphilus lacydonensis , and Tessaracoccus were significantly increased in both PC and RC. Conclusions Urinary microbiome composition was different depending on the xlink:type of genitourinary malignancies, and we identified bacteria that are significantly associated with each xlink:type of malignancy. Specifically, several bacterial species were associated both PC and RC, suggesting that PC and RC share a similar pathogenesis-related urinary microbiome.