Benthic foraminifera are excellent indicators of marine environmental quality due to their wide distribution, small size and large abundance, high species diversity, short life cycle, good preservation potential in marine sediments, and high sensitivity to environmental changes. Traditional monitoring of benthic foraminifera is mainly based on morphology, but this process is time-consuming, labor-intensive, and makes it difficult to detect some species with small individuals and low abundance. The investigation method based on DNA sequencing, with its advantages of high efficiency, high sensitivity, and environmentally friendly, provides a new way to identify benthic foraminifera species and assess community diversity. This paper reviews the progress of DNA sequencing technology in species identification and classification, community structure and diversity investigation, and identification of symbionts in large benthic foraminifera. As there are some technical limitations of DNA sequencing in benthic foraminifera monitoring, such as lack of standardized operation process, imperfection of reference databases, impossibility of absolute quantification of benthic foraminifera abundance, and overestimation of community diversity, optimization can be achieved by formulating a standardized and unified operation process, establishing an open and shared benthic foraminifera reference database, and combining the method with fluorescence quantitative PCR and environmental RNA sequencing technology. In the future, development and innovation of gene sequencing technology should be strengthened to explore the potential of DNA sequencing technology in benthic foraminifera monitoring in a detailed manner.