According to 16S rRNA gene- or genome-based phylogeny, magnetotactic bacteria (MTB) belong to diverse taxonomic groups. Here we analyzed the diversity of MTB in a sample taken from the freshwater Lake Beloe Bordukovskoe near Moscow, Russia, by using molecular identification based on sequencing of the 16S rRNA gene and mamK, a specific marker gene for these bacteria. A protein encoded by the mamK gene is involved in magnetosome chain arrangement inside the cell. As a result, six operational taxonomic units (OTUs) of MTB were identified. Among them, OTUs affiliated with the phylum Nitrospirae were predominant. ‘Ca. Etaproteobacteria’ and Alphaproteobacteria represented the minor groups of MTB. We also identified a novel MTB belonging to the family Syntrophaceae of the Deltaproteobacteria class. Using a combination of fluorescence and transmission electron microscopy, the bacteria belonging to these new MTB groups were visualized. Electron microscopy revealed that Syntrophaceae MTB were rod-shaped and synthesized elongated magnetosomes, arranged as a disorganized cluster. Among the Nitrospirae group, two groups with vibrioid cell shape and one group of ovoid-shaped bacteria were identified, all of which had elongated magnetosome crystals consisting of magnetite.