A microorganism separation system comprising a sample solution container 34 containing microorganisms, a separator 1, and a receiver 47, designed to separate microorganisms from the sample solution; further comprising a microorganism detection sensor and a plate 49 which has a plurality of receivers 47 connected to each other and an identification indicator, wherein when the microorganism detection sensor judges that a microorganism has passed, supply of the sample solution is stopped, the detected microorganism is discharged together with the sample solution, and then the solution starts to be injected into the receiver; and, the number of times microorganisms are detected during the time period from the start of the injection to the end is recognized as separation quantity; and then as separation information, the separation quantity, number for a receiver 47 into which a microorganism was injected for each identification indicator, signal waveform sent from the microorganism detection sensor at the separation, date and temperature are stored.