There have been many studies linking the microbiome to disease, including cancer. The microbiome is all the genetic material in the form of bacteria, fungi, or viruses that exists in parts of the human body. The microbiome is reported to trigger cancer due to the presence of certain pathogenic microbes or the presence of dysbiosis. Therefore, it is necessary to analyze the diversity of the microbiome to see the relationship. Metagenomics is the latest technology that can be used to analyze the diversity of the microbiome in cancer. There are two approaches in metagenomic analysis, namely targeted sequencing and sequencing of the entire metagenome. This paper will discuss a targeted sequencing metagenomic approach for the identification of microbial diversity in cancer.