Recent trends in flow cytometry have established new techniques in bacteriology. Advances in fluorescent dye technology complement these improvements, offering probes for a variety of cellular functions. Bacterial ecology requires the application of new techniques to help answer questions unanswerable by traditional methods alone. Here we review some aspects of how coupling the two technologies has enabled researchers to directly study individual bacterial cells, and revealed the complexity and heterogeneity present in both laboratory cultures and in environmental samples. Results are discussed with respect to viability analysis, stress induced changes, specific cell detection and cell sorting.