A highly sensitive fluorescence resonance energy transfer (FRET)-based quantum dot (QD)-Aptasensor was developed for microcystin-LR (MC-LR) detection in eutrophic water. The FRET-based QD-Aptasensor was able to achieve an analytical limit of detection of 10(-4) mu g/L MC-LR with selectivity among different congeners (microcystin-YR, microcystin-LY, microcystin-LW, microcystin-RR, microcystin-LF, microcystin-LA, and Nodularin). The performance of QD-Aptasensor was demonstrated using both laboratory grown cyanobacterial culture (Microcystis aeruginosa) and environmental water samples. For the laboratory culture, the intracellular MC-LR concentrations changed according to the cyanobacterial growth curve. The QD-Aptasensor detected MC-LR up to 12.7-15.8 mu g/L-cyanobacterial culture at early stationary phase. For the environmental samples, the MC-LR was measured at cell densities of 2.7x10(8) and 6.6x10(10) cells/L-water, which correspond to 1.0 and 7.2 mu g MC-LR/L-water, respectively. For comparison, the laboratory culture and environmental samples were analyzed by the conventional enzyme-linked immuno-sorbent assay (ELISA). The MC-LR concentrations of FRET-based QD-Aptasensor showed a strong positive correlation with those of ELISA (Pearson correlation coefficient, r = 0.981 and r = 0.862) for the laboratory culture and environmental samples, respectively.