Advances in nanotechnology increasingly rely on characterization tools with atomic resolution. Chemical information on hetero-geneous nanostructures in particular is more and more crucial for diagnosing and predicting properties of novel functional nanodevices. We have developed an analytical electron microscope enabling elemental analysis at the sub-nanometer region which is a powerful tool to determine the atomic structures in nano-materials. Single-atom identification has been demonstrated by this apparatus for the chemically decorated carbon nanostructures with the highest confidence level.