Rapid, sensitive, and selective detection of infectious agents in food, water, the environment, and patient samples is critical for appropriate countermeasures, particularly in the event of a suspected outbreak. The biosensors should be inexpensive, portable, and easy to use, require minimal sample preparation and reagents, and should be able to detect emerging variants for wide acceptance. The vast number of biological threats, each with its own unique characteristics, as well as the stringent requirements of a biosensor, dictates a multidisciplinary approach to overcome the scientific and technological hurdles necessary to develop a "real-time" biosensor. While advances in several areas are required, one of the most critical components of a biosensor is the recognition molecule. Ultimately, the success of a biosensor is highly dependent on the specificity, sensitivity, reproducibility, and broad applicability of the recognition element. In this chapter, we review the state-of-the-art advancements in the molecular recognition of toxins and pathogens. We discuss different recognition molecules in detail with particular emphasis on the use of emerging recognition molecules that include antimicrobial peptides, carbohydrates, molecularly imprinted polymers, aptamers, and phage for detection of infectious agents. As this chapter indicates, there are advantages and limitations to each molecule. However, significant advances in the area of molecular recognition for toxins and pathogens are being made. As the field evolves, continued improvements in molecular recognition and other components of the biosensor such as transducer Chemosensors: Principles, Strategies, and Applications, First Edition. Edited by Binghe Wang and Eric V. Anslyn.