New initiatives put forward by clinical diagnosis require the development of technologies for high throughput screening (HTS) of multiple analytes. Suspension arrays have great advantages over the planar arraybased multiplexing assays, and the encoded bead is the key for providing multiplexing capability. Among various encoding strategies, optically encoded microspheres have been widely used while the number of codes is still limited. This review discusses the progress of optical encoding strategy from mainly three aspects, namely organic dyes, quantum dots (QDs) and surface-enhanced Raman scattering (SERS) active substrates. Emphases are put up on describing how these optical encoded microbeads are manufactured and the merits and demerits of different encoding materials are compared.