Method and apparatus for the detection of microbes in liquids, in air and on non-living surfaces in which samples are exposed to frequency-modulated electromagnetic radiation of specific energies capable of exciting various metabolites, cofactors and cellular and spore components, with the microbial cells to be sampled (and more specifically the excited metabolites, cofactors and/or other cellular components) contained therein emit fluorescence that can be measured that is similarly frequency-modulated provided that the excitation frequencies are longer than the fluorescence lifetime of the excited intrinsic microbial fluorophore. The contribution to the measured signal due to each excitation frequency resulting from microbial intrinsic fluorescence is determined with a method capable of calculating the intensity of each frequency-modulated signal, and the relative total fluorescent signals of the intrinsic microbial components associated with each excitation frequency are required to lie within physiological ranges, with the amplitude of the fluorescence signals used to enumerate the microbe content in the sample.