Nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) are two types of magnetic resonance (MR) spectroscopy that has been used to study physical and chemical of agriculture inputs and products; biomass; and environmental organic matter, such as soil, sedimentary and aquatic organic matter. Both techniques are very useful in agricultural sciences—highlighting NMR applications—to understand the constitution, properties, functionality, and quality of food and nonfood crops and soil organic matter, contributing to improve the productive systems related to the agroindustrial chains. This chapter deals with the physical phenomena involved in each one, their uses in agriculture and some examples of practical uses.