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In the last 15 years there has been a revolution in the application of nucleic acid based techniques to the detection of micro-organisms. This paper considers the activities in 2 current projects supported by AwwaRF and the CRC for Water Quality and Treatment that rely heavily on these techniques for the detection of toxic blue-green algae (cyanobacteria) and production of the taste and odor compounds methylisoborneol (MIB) and geosmin. Includes 4 references.