The characteristics of micro-scale vertical heterogeneity of physicochemical parameters, photosynthetic pigments’ content and populations of phototrophic microbial plankton in four karst lakes of the Mari-Chodra NP (rep. Mari El), the Bolshoy Kichier, Cherny Kichier, Shungaldan and the Blue Oxbow, are presented on the basis of summer surveys of 2006, 2007 and 2009. According to our data, two lakes, Shungaldan and Cherny Kichier are, meromictic waterbodies of crenogenic type; the Lake Bolshoy Kichier is holomictic with stable summer stratification and anoxic hypolimnion. The Lake Blue Oxbow occupies an intermediate position, and, apparently, is irregularly mixing. The physicochemical conditions and composition of the phototrophic plankton communities of the chemocline zone of the two previously studied lakes, Bolshoy and Cherny Kichier, have remained stable over the past 20-35 years. Significant development of anoxygenic phototrophic bacteria was found in two lakes in which data on their development were previously absent. In the bacterial plates of meromictic lakes, the concentration of bacteriochlorophyll d, the pigment of green phototrophic bacteria, reaches some mg per liter.