Dense populations of anaerobic bacteria were found sequentially layered below the thermocline in two eutrophic lakes in southwest Michigan. Phase and electron microscopy of whole cells and thin sections were used to reveal the in situ morphology of the dominant members of the community. The predominant chlorophyll-containing bacteria were identified on the basis of their morphology to be members of the genera Pelodictyon, Prosthecochloris, Clathrochloris, Chlorochromatium, Pelochromatium, Thiopedia, Thiocystis, Thiospirillum, and Chromatium. The natural morphology of these organisms is described and compared with the morphology of reported isolates; the morphology of unisolated genera was compared with previous descriptions of natural samples. Most of the organisms near the sediment–water interface and two from the upper hypolimnion have not been previously described. They have been divided into six distinct groups based on morphology; the morphological features of each group are presented. This approach, based on the morphological uniqueness of the procaryotes present, provides a satisfactory method for grouping members of the hypolimnetic community for ecological studies.