Abstract A method for the isolation of manganese-oxidizing pedomicrobia from water is described. The method employs a combination of growth on a manganese containing indicator medium and micromanipulation. Pedomicrobia are slow-growing and are frequently overgrown by spreading bacteria. Colonies of manganese-oxidizing strains are easily detected at an early stage of development because of the accumulation of black manganese oxide. Micromanipulation allows selection of cells from microcolonies before they are overgrown. The procedure has been successfully used to isolate manganese-oxidizing Pedomicrobium cultures from water distribution systems experiencing persistent manganese-related dirty water problems. Considerable savings in time and materials have been made compared with conventional dilution plating techniques.