The discovery of intratumoral microbiota has led to research uncovering their diversity, their colonization of the tumor microenvironment, and their impact on anticancer immunity. These discoveries can be used for diagnosis and utilized for therapeutic strategies such as immunotherapy in cancer. The impact of intratumoral microorganisms on cancerogenesis, the tumor microenvironment, and immune response, are highly species-specific and many relationships still need to be elucidated. To unravel some of these mechanisms we assessed intratumoral bacteria, fungi, and viruses in ovarian serous cystadenocarcinoma (OV) and pancreatic adenocarcinoma (PAAD) from RNA sequencing data of The Cancer Genome Atlas. Diversity within and between samples was calculated, revealing that microbial diversity is more dependent on tissue of origin than tumor occurrence. The abundance of different species correlated with several immune cell types and diverse immune pathways. In addition, we identified microbial peptides, which could trigger an anti-tumoral immune response by similarity to tumor associated antigens, termed molecular mimicry. Several microorganisms in OV were discovered to form a correlation cluster with immune cells, including tumor promoting M2 macrophages. The impact of microbial abundance on patient survival was investigated, and two species were found to have an impact on overall survival in OV and in PAAD, respectively. By overlapping all analyses, the most interesting species were the fungus Verticillium dahliae in OV and the bacterium Actinomyces succiniciruminis in PAAD, which could play an important role in the respective cancer. In summary, this work has provided a basis for how intratumoral bacteria, fungi and viruses can be assessed based on RNA sequencing data, and has highlighted potential links to antitumor immunity.