Comparative surface imaging was performed on uncoated fungal spores and stained section-face by field emission scanning electron microscopy with an in-column energy-selective backscattered electron detector. Epoxy resin thin sections (ca. 200 and 500 nm thick) of the osmicated and uranyl acetate/lead citrate-stained fungus were examined with the microscope. Topographical contrast was evident in secondary electron imaging by either a below-lens or an in-lens detector. Meanwhile, low-loss backscattered electron images showed mainly compositional contrast at low accelerating voltages (mostly below 1 kV). With attenuated topographical contrast, several different electron densities could be detected, exhibiting several levels of electron density even on a flat plane of spines. Minute differences in topography on epoxy resin sections as seen by secondary electron imaging represented the periphery of the fungal spores and hyphae. On the other hand, the compositional contrast could be retrieved from stained section-face in low-loss BSE imaging, revealing subcellular entities after contrast inversion. The resolution of low-loss BSE imaging was sufficient to resolve plasma membrane, and various types of vacuoles and vesicles. These results suggest that low-loss backscattered electron imaging could potentially provide compositional information to resolve surface chemical features of uncoated microbial cells and stained section-face with heterogeneous surface compositions.