An apparatus and a method for electromagnetically detecting microorganisms. The apparatus includes a pair of first electrodes which are positioned to be opposite to each other on a measuring cell and are connected to a power supply to generate an electric field around a solution contained in the measuring cell, a magnetic field generating unit which generates a magnetic field around the solution contained in the measuring cell in a perpendicular direction to the electric field, second electrodes which are positioned perpendicularly to both the electric field and the magnetic field, and a voltage measurer which measures the voltage generated between the second electrodes as the microorganisms move in the measuring cell. The apparatus determines the presence, quantity and identity of microorganisms with negative surface charge with improved sensitivity using the Hall effect.