Conventional analytical methods based on the detection of a single disease marker may not be sufficiently accurate because the progression of disease generally involves multiple chemicals and biomolecules. The drive for simultaneous analysis of multiple targets, which plays a key role in both basic biomedical research and clinical applications, demands the development of multiplexed bioassays with high‐throughput. In this minireview, we summarize the recent progress in optical multiplexed analytical techniques for improving biomedical diagnostics, in which fluorescence and surface enhanced Raman scattering (SERS) with distinctive optical features are chosen as the main readout signals. Focusing on multiplexed strategies in the biomedical field, a selection of recent contributions from biosensing of multiple analytes and multicolor cellular tracking to in vivo multiplexed bioimaging are highlighted. Finally, we frame the future challenges and opportunities for multiplexed bioanalysis.