Diffusion MRI (dMRI) is an important imaging modality that is used extensively to diagnose and monitor diseases. dMRI measures random motion of water molecules and helps elucidate microstructural properties of tissues. Optimal diffusion encoding paradigms have been developed to reduce acquisition time, minimize artifacts, and acquire high fidelity data needed for advanced modeling of tissue properties. To further probe microstructural properties, joint diffusion-relaxometry and diffusion weighted MR fingerprinting have garnered interest. A thorough knowledge of different diffusion encoding methods is essential to accurately encode diffusion in MR experiments. Here, we review fundamental physics of diffusion encoding methods, their associated challenges, and how to address them. Advanced diffusion acquisition methods are also discussed.