A microorganism testing apparatus for measuring the number of microorganisms in a sample solution, the microorganism testing apparatus comprising: a stirring unit (2, 5, 6, 7) for performing stirring of the sample solution and batch-type sample container formed of material transmitting light to which a sample and a fluorescent staining reagent are added; the apparatus further comprising: an excitation light source provided with a plurality of light sources for emitting excitation light to irradiate a surface of the sample container while the sample solution is being continuously stirred by the stirring unit; a photodetector for detecting fluorescence light emission from the sample caused by the excitation light from the excitation light source; processing means processing the electrical signals obtained from the light detected by the photodetector to detect and count the number of light emissions, and to calculate the number of microorganisms included in the sample within the sample container from the number of light emissions; and an operation unit electrically connected to the processing means; wherein the excitation light source comprises two different kinds of excitation light sources (8a, 8b), the excitation light sources being a first light source emitting light with a wavelength region causing phytoplankton to emit chlorophyll fluorescence and a second light source emitting light with a wavelength region causing microorganisms stained by the fluorescent staining reagent to emit fluorescence; wherein the processing means comprises a calculating unit calculating a number of microorganisms N with respect to a permissible ballast water discharge criterion by determining each of a microbial population n1 acquired from chlorophyll fluorescence emission of the sample without the staining reagent and on excitation by the first light source alone, a microbial population n2 acquired from fluorescence emission by the fluorescent staining reagent after staining of the sample with the staining reagent and on excitation by the second light source alone and a microbial population n3 acquired from both of the chlorophyll fluorescence emission and the fluorescence emission by the fluorescent staining reagent after staining of the sample with the staining reagent and on simultaneous excitation by both of the first and second light sources. an excitation light source provided with a plurality of light sources for emitting excitation light to irradiate a surface of the sample container while the sample solution is being continuously stirred by the stirring unit; a photodetector for detecting fluorescence light emission from the sample caused by the excitation light from the excitation light source; processing means processing the electrical signals obtained from the light detected by the photodetector to detect and count the number of light emissions, and to calculate the number of microorganisms included in the sample within the sample container from the number of light emissions; and an operation unit electrically connected to the processing means; wherein the excitation light source comprises two different kinds of excitation light sources (8a, 8b), the excitation light sources being a first light source emitting light with a wavelength region causing phytoplankton to emit chlorophyll fluorescence and a second light source emitting light with a wavelength region causing microorganisms stained by the fluorescent staining reagent to emit fluorescence; wherein the processing means comprises a calculating unit calculating a number of microorganisms N with respect to a permissible ballast water discharge criterion by determining each of a microbial population n1 acquired from chlorophyll fluorescence emission of the sample without the staining reagent and on excitation by the first light source alone, a microbial population n2 acquired from fluorescence emission by the fluorescent staining reagent after staining of the sample with the staining reagent and on excitation by the second light source alone and a microbial population n3 acquired from both of the chlorophyll fluorescence emission and the fluorescence emission by the fluorescent staining reagent after staining of the sample with the staining reagent and on simultaneous excitation by both of the first and second light sources.