With the increasing demand for multiplex and high-throughput analysis of large numbers of biomolecules, multiplex technology becomes a promising tool for carrying out thousands of individual reactions at the same time for large-scale biological analysis. Among current technologies, suspension arrays based on appropriate barcode particles have been popularly used in multiplex bioassays of many research fields with the ability of unique encoding, such as in the clinical, medicinal, nutritional, and environmental fields. Besides the unique form of barcode, these particles have higher flexibility, better sensitivity, and faster reaction kinetics. In this review, we present some examples of typical barcode particles that are divided into different groups depending on how they are encoded and their applications in multiplex bioassays for different targets such as proteins, DNA and RNA sequences, and cells. The bioassays for monitoring food safety, drug research, and clinical diagnosis are also described.