Protein ubiquitination is one of the most versatile post-translational modifications, and is widely involved in multiple cellular processes including protein degradation, cellular signaling transduction and DNA damage responses. The eight sites (M1, K6, K11, K27, K29, K33, K48, K63) of ubiquitin help to form individual complex chains by being attached to C-terminus of another ubiquitin molecule. In addition, these different ubiquitin chains play distinct biological functions. However, functions of most ubiquitin chain types are poorly understood, due to the lack of tools that enable ubiquitin linkage-specific detection. Affinity reagents such as ubiquitin linkage-specific antibodies are powerful tools for the studies of the ubiquitin chains. This review focuses on the development and applications of several ubiquitin linkage-specific antibodies, as well as other specific affinity tools, which can be used for identifying of ubiquitin chains such as Affimer and UBD-based fluorescent sensors proteins. This review also briefly introduces the methods of obtaining antigens for the discovery of these ubiquitin linkage-specific antibodies.