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AbstractBased on biomolecular methods, rapid and selective identification of human pathogenic water organisms becomes an important issue. Legionella spp., are pathogenic water bacteria with worldwide significance. Prevalent detection methods for these microorganisms are time and/or cost intensive. We describe a detection setup and relating DNA assay. A miniaturized real‐time polymerase chain reaction (real‐time PCR) for direct on‐line discrimination of Legionella pneumophila and Legionella spp. was established and integrated into a real‐time PCR‐chip‐system. The PCR‐chip device combines a temperature controlling unit and a fluorescence intensity measurement. It was designed to achieve rapid amplification, using an approach of real‐time fluorescence read out with the intercalating dye EvaGreen® and melting curve analysis, without requiring multiple probes. The presented results exhibit reproducibility and good sensitivity, showing that the setup is suitable for robust, rapid and cost‐efficient detection and monitoring of a variety of Legionella spp.in urban water samples.