Analyses with a scanning transmission x-ray microscope (STXM) using x-ray absorption near edge structure (XANES) spectroscopy were applied for the molecular characterization of two kinds of carbonaceous particles of unknown origin, termed category 3, which were collected from the Hayabusa spacecraft sample catcher. Carbon-XANES spectra of the category 3 particles displayed typical spectral patterns of heterogeneous organic macromolecules; peaks corresponding to aromatic/olefinic carbon, heterocyclic nitrogen and/or nitrile, and carboxyl carbon were all detected. Nitrogen-XANES spectra of the particles showed the presence of N-functional groups such as imine, nitrile, aromatic nitrogen, amide, pyrrole, and amine. An oxygen-XANES spectrum of one of the particles showed a ketone group. Differences in carbon-and nitrogen-XANES spectra of the category 3 particles before and after transmission electron microscopic (TEM) observations were observed, which demonstrates that the carbonaceous materials are electron beam sensitive. Calcium-XANES spectroscopy and elemental contrast mapping identified a calcium carbonate grain from one of the category 3 particles. No fluorine-containing molecular species were detected in fluorine-XANES spectra of the particles. The organic macromolecular features of the category 3 particles were distinct from commercial and/or biological 'fresh (non-degraded)' polymers, but the category 3 molecular features could possibly reflect degradation of contaminant polymer materials or polymer materials used on the Hayabusa spacecraft. However, an extraterrestrial origin for these materials cannot currently be ruled out.