Aptamers are an alternative affinity reagent approach to antibodies that track and inhibit small molecule targets such as proteins. The current method of aptamer discovery is time-consuming and, with over 24,000 proteins in the human proteome alone, is not suitable to address the growing need for high-quality affinity reagents.  The aptamer discovery process could be improved through coupling a new method of aptamer selection with advanced flow cytometry techniques. This new method of aptamer discovery involves a random library (>10¹² sequences) of single-stranded DNA that is first exposed to individual fluorescent targets in order to allow target-specific aptamer sequences to bind. Those target-bound sequences are separated using a single-variable sort gate with a fluorescence-activated cell sorter (FACS), amplified, and the process is repeated until the pool has converged to a small number of high-affinity binders. In our novel approach, two libraries pre-biased towards two protein targets are combined in order to select for multiple specific aptamers simultaneously.  Using FACS, we can separate aptamers using multiple levels of stringency in order to find aptamers with finely tuned binding properties.  After several cycles of co-evolving sequences, which bind to one or both targets, it is expected that we will have several highly specific aptamers towards our two protein targets.  In the future, this process could potentially be expanded to develop aptamers against numerous targets at the same time.