In this study, we investigate the molecular structural characteristics of organic remains in various cellular organelles from a 180 Ma Jurassic royal fern belonging to the Osmundaceae family of ferns, and compare their carbon isotopic compositions to a now-living species of royal fern (Osmunda regalis). We discovered molecular structural variations indicated by Raman and infrared spectral parameters obtained from various fossilized cellular organelles. The organic remains preserved in the chromosomes and cell nuclei show marked structural heterogeneities compared to the cell walls during different stages of the cell cycle. The fossil and extant fern have similar δ13C values obtained from bulk samples, supporting evolutionary stasis in this plant lineage and an unchanged metabolic pathway of carbon assimilation since the Jurassic. The organic remains in the cellular organelles of the fossil seem to be less heterogeneous than those in the extant fern, likely due to the preferential preservation of certain cellular compounds during fossilization. Taphonomic processes appear to have diminished the subcellular isotopic heterogeneities. Our research sheds light on the functioning of ancient plant cellular organelles during mitosis, provides insights to the taphonomic processes operating at molecular and isotopic levels, and shows the practicability of in situ techniques in studying the evolution and behaviors of ancient cells.