Flow cytometry was used to count bac-of this study showed that flow cytometry terial cells from diverse origins: one was a reliable technique for counting a strain of E. coli, one sample of lake water, mixture of bacteria in samples from and 18 samples of estuary water. To verify the accuracy and the precision of this technique, total bacteria counts made by flow cytometry were compared with counts by direct observation using epifluorescence microscopy. The results aquatic ecosystems.Key terms: Bacteria, enumeration, flow cytometry, epifluorescence microscopy, aquatic ecosystems Bacterial abundances in water samples are usually estimated by the indirect method of growing the bacterial cells in culture medium. The selective specificity of culture media can permit both the counting and the qualification of a certain population of bacteria (e.g., Escherichia coli) among a bacterial community. Even the least specific culture media is still selective with respect to total bacterial cell numbers in a sample. For example, a nutrient agar allows only the growth of heterotrophic bacteria. However, the selective pressure of the culture media (e.g., the presence of 2-3-5 triphenyl tetrazolium chloride towards E . coli) can prohibit the development of a certain number of cells that are stressed but not dead, and that should develop in the medium. Thus there is a n underestimation of bacterial abundance. A second, more direct method to estimate bacterial populations is the technique of epifluorescence microscopy. Coupled with a fluorochrome dye to stain cells, epifluorescence microscopy allows the enumeration of all bacterial cells in a water sample. This direct counting method is especially important in bacterial ecology for determining total bacterial numbers in aquatic ecosystems. However, this method is both time consuming and tedious if one is to have a high level of precision in the estimation of bacterial abundances (12). The technique of flow cytometry permits the quantification of physical and biochemical aspects of individual cells. This technique has been verified for the analysis of reference bacterial populations using fluorochrome dyes (ethydium bromide and mithramycin) (10, 11) and for the detection of pathogenic bacteria in milk, blood, and cooling tower waters using fluorescent antibodies and fluorochrome dyes (1,3,13). Recently, flow cytometry has been used to characterize bacterial communities in aquatic ecosystems according to cell size and relative DNA content (6).