The outbreak of pathogens has not only caused huge losses, but also seriously hindered the healthy and sustainable development of the artificial breeding industry. Therefore, it is urgent to develop rapid detection technology and pathogen prevention and control technology for pathogens to prevent the outbreak of diseases. Aptamer is the functional single-stranded oligonucleotide with high affinity and specificity for specific targets and screening by systematic evolution of ligands by exponential enrichment (SELEX). Based on domestic and foreign research, this paper described the advantages of aptamers and their research progress in the prevention and control of pathogenic microorganisms in farmed animals, and focused on five challenges in the application of aptamers. (1) The limitations of aptamer screening technology. (2) The lack of stability and safety of aptamers in therapeutic applications. (3) The sustainability of aptamers in organisms with targeted therapeutic effects. (4) The need to improve the accuracy of aptamers in vivo experiments. (5) The possibility of cascading aptamers with other assays to build a comprehensive testing platform. At present, the research of aptamers on cultured animal pathogens has just started, and it has broad application prospects in rapid detection and targeted therapy.