Microbes in biofilms are generally found to be resistant to antimicrobial agents. One set of hypotheses attributes biofilm resistance to acquisition of special physiological traits (phenotypic resistance). Methods are presented that allow discrimination of subpopulations of Candida albicans cells that exhibit relative levels of phenotypic resistance to chlorhexidine. The assay for phenotypic resistance is based on microscopic detection of the rate of penetration of propidium iodide (PI) into single cells as their membranes become disrupted by chlorhexidine. Using the assay, it was found that batch cultures became progressively more resistant to the action of chlorhexidine during the transition from exponential growth to early stationary phase. Results are presented demonstrating that the methods can be used to characterize relative levels of phenotypic resistance exhibited by cells at the base of a C. albicans biofilm.