Magnetotactic bacteria from aquatic environments were analyzed with the electron spectroscopic imaging technique. Rod-shaped bacteria and cocci were present in most of the samples observed. Magnetotactic multicellular aggregates were also observed at some of the sampling sites. The use of electron spectroscopic imaging allowed the observation of magnetosomes inside magnetotactic microorganisms with exceptional clarity. The number, size, and morphology of magnetosomes, as well as their ultrastructural spatial disposition inside the bacterial cell, could be directly observed and associated with the disposition of flagella of the respective cells.This allowed us to examine the structural relationships between magnetosomes and flagella, which are important components in the mechanisms of magnetotaxis. In disrupted magnetotactic multicellular aggregates, connections between cells were also visualized. We believe this technique will be useful in studying not only magnetotactic bacteria but also other uncultured microorganisms from natural environments.