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Microcystins are a family of potent toxic oligopeptides produced by freshwater cyanobacteria genera and have been a great threat to the welfare of humans and animals. There has been a great demand for developing a fast and convenient analytical method to detect microcystins. Recently, direct competition ELISA using monoclonal or polyclonal antibody has become the prevailing method for detecting microcystins. In this study, we report rapid quantification methods of microcystins using fluorescence for a detection signal and a lateral-flow-type immunochromatography as a separation system. The assay systems consist of a test strip housed in a disposable cartridge and a portable laser-fluorescence scanner. The components of a test strip are as follows: a nitrocellulose membrane, a sample pad, an absorption pad, and a backing card. A fluorescence scanner was designed to fit the cartridge and to quantify the distribution of the fluorescence intensity along the strip. When the calibration curve for an antibody-immobilized system was determined, a good linearity was displayed in the range from 125 to 2000 pg/mL of microcystin-LR. The linear-regression coefficient (R) was 0.938 between relative fluorescence intensity and the microcystin concentration. The limit of detection was determined to be 95.38 pg/mL. We then designed another biosensor system by changing an experimental format from the competition type to the inhibition type. When compared to the antibody-immobilized system, the antigen-immobilized assay detected a lower level of microcystin but did not discern microcystin-LR above 1000 pg/mL. The detection of limit for the antigen-immobilized system was 47.23 pg/mL. The linear regression coefficient (R) in the antigen-immobilized system equaled to 0.927. The reproducibility in the antigen-immobilized system was good through the entire range. The reproducibility in the antibody-immobilized system was relatively poor when compared to a MC-immobilized system. However, it still registered in the acceptable range of 7.32−9.91% except for the extreme ends of the MC concentration. Finally, surface water was tested to check for potential matrix interference. The calibration curve displayed a similar pattern as did those for other matrixes, including PBS and tap water, although its sensitivity was a little less due to the interference with certain components in the surface water. Overall, either of the biosensor systems can be used as a useful on-site detection tool for checking drinking water or surface water for microcystins. The laser-fluorescence scanner we developed is relatively small, transportable, and easy to use. Thus, the samples can be analyzed for microcystins at the test site using a real-time base within 15 min without having to bring the samples back to the laboratory.