Fully-automated detection system for manipulation of bloom-forming genera of cyanobacteria, Microcystis spp., was developed using a specific DNA probe designed based on sequence polymorphism within the 16S ribosomal DNA (rDNA) of this strain, Specific DNA sequences in 16S rDNA for Microcystis spp were determined by sequence data analysis and two probes were designed for detection of Microcystis spp, Microcystis 16S rDNA was amplified by PCR and applied to the detection system where target DNA was selectively recognized by species-specific hybridization using two DNA probes, a DNA probe conjugated on magnetic particles and a digoxigenin-labeled DNA probe. Using alkaline phosphatase labeled anti-digoxigenin antibody probe, target DNA can be detected by luminescence. In this detection method, the difference in only a few base pairs of target DNA can be discriminated and specific detection of Microcystis spp. was achieved. The appropriate annealing temperature was 60 degrees C. A computer controlled fully-automated system was used for detection of Microcystis spp and detection efficiency equivalent to that of a manual approach was obtained.