Single particle tracking can reveal dynamic information at the scale of single molecules in living cells but thus far has been limited either in the range of potential protein targets or in the quality and number of tracks attainable. We demonstrate a new approach to single molecule tracking by using the blinking properties of synthetic dyes targeted to proteins of interest with genetically encoded tags to generate high-density tracks while maintaining flexibility in protein labeling. We track membrane proteins using different combinations of dyes and show that the concept can be extended to three-color imaging. Moreover, we show that this technique is not limited to the membrane by performing live tracking of proteins in intracellular compartments.