Pathogenic microorganisms caused infectious diseases such as viruses and bacteria pose great threat to human health. Although significant progress has been obtained in the diagnosis and prevention of infectious diseases, it still remains challenging to develop rapid and cost-effective detection approaches and overcome the side effects of therapeutic agents and pathogen resistance. Functional nucleic acids (FNAs), especially the most widely used aptamers and DNAzymes, hold the advantages of high stability and flexible design, which make them ideal molecular recognition tools for bacteria and viruses, whole bacteria and viruses, and potential therapeutic drugs for infectious disease. This review summarizes important advances in the selection and detection of bacteria and viruses associated FNAs, as well as their potential prevention ability of infectious disease in recent years. Finally, the challenges and future development directions are concluded.