The meromictic Lake Cadagno is characterized by a compact chemocline with high concentration of anoxygenic phototrophic purple sulfur bacteria (PSB) and green sulfur bacteria (GSB). The co-occurrence of PSB and GSB in the same ecological niche makes the chemocline of Lake Cadagno an ideal system for studying the conditions and consequences of coexistence of photosynthetic bacteria population. In this study, flow cytometry (FCM) was applied as a fast tool to identify metabolic changes due to the production and consumption of inclusion bodies and to follow population dynamics of closely related anoxygenic photosynthetic sulfur bacteria in their natural environment. Through this technique the large-celled PSB Chromatium okenii and GSB Chlorobium populations were reliably separated and identified due to difference in auto-fluorescence and cell size. Moreover, we showed that these dominant taxa share the same ecological niche. Two mechanisms for this coexistence were proposed: population activity alternation and bioconvection.