In this report the correlation between the solution photoluminescence (PL) quantum yield and the fluorescence emission of individual semiconductor quantum dots (QDs) is investigated. This is done by taking advantage of previously reported enhancement in the macroscopic quantum yield of water-soluble QDs capped with dihydrolipoic acid (DHLA) when self-assembled with polyhistidine-appended proteins, and by using fluorescence coincidence analysis (FCA) to detect the presence of “bright” and “dark” single QDs in solution. This allows for changes in the fraction of the two QD species to be tracked as the PL yield of the solution is progressively altered. The results clearly indicate that in a dispersion of luminescent nanocrystals, “bright” (intermittently emitting) single QDs coexist with “permanently dark” (non-emitting) QDs. Furthermore, the increase in the fraction of emitting QDs accompanies the increase in the PL quantum yield of the solution. These findings support the idea that a dispersion of QDs consists of two optically distinct populations of nanocrystals—one is “bright” while the other is “dark;” and that the relative fraction of these two populations defines the overall PL yield.