An object of the present invention is to provide a counting method of microbial populations and a counting system of the microbial populations which can shorten the counting time by using a chaotic wave sensor. One embodiment of the present invention provides the counting method of the microbial populations, which comprises the following steps of: preparing a sample placement unit having a plurality of divided cells each containing a culture material; distributing a sample to be measured to the plurality of divided cells; sequentially irradiating waves to the plurality of divided cells; sequentially detecting individual wave information emitted from samples accommodated in each divided cell in association with the sequentially irradiated wave; determining presence or absence of microorganisms in each divided cell by using the individual wave information; and calculating the microbial populations in the sample using the number of divided cells in which the microorganisms are present.