Accurate monitoring and identification of Legionella species, the causative agents of Legionnaires' and other diseases, in environmental water sources is an important public health issue. Traditional culture methods often lack the sensitivity and specificity that can be attained using the polymerase chain reaction (PCR) to amplify targeted regions of the bacterial genome. Matrix‐assisted laser desorption/ionization combined with time‐of‐flight (MALDI‐TOF) mass spectrometry is shown to be useful for detection of 108‐ and 168‐base PCR products specific to Legionella. A rapid purification aimed at removal of salts and unreacted primers is demonstrated. The addition of a synthetic DNA 20‐mer to the MALDI sample facilitates aiming the laser at a favorable spot on the sample probe from which the PCR products can be detected.