Crystallographic structures of spheroidal graphite particles (graphite nodules) were examined using transmission electron microscopy (TEM). Structures of graphite nodules were investigated relative to different stages of nodule growth in ductile iron. Curved graphene layers were observed during the early growth of the graphite nodules. Thin layered stacking faults give rise to streaking in the basal reflections, which give rise to curvature of the nodule and growth steps on the surface. Columnar substructures consisting of parallel peripheral subgrains were found in the outside region of graphite nodules that were formed during the intermediate growth stage. Straight planar graphene layers were observed in the columnar substructures. Crystallographic orientation of graphite showed little change through the subgrain and the c-axes of multiple subgrains in a single columnar substructure were parallel. A method for characterizing the crystal structures of graphite based on the selected area diffraction pattern was introduced. Both hexagonal structure and rhombohedral structure were found in the spheroidal graphite particles. Possible crystallographic defects associated with hexagonal-rhombohedral structure transition were discussed.