Analytical questions relating to the influence of sedimentation on the preservation states of Carboniferous plant fossils are seldom addressed in the literature. Here we address specifically the influence facies differences have on preservation states and suggest how they can be analyzed. The case study involves the seed fern Neuropteris ovata (Hoffmann) that occurs as opaque pinnules in the roof shale and as transparent pinnules in an associated crevasse-splay of the basal Cantabrian in age, Point Aconi Coal Seam, Sydney Coalfield, Canada. The color differences imply different molecular pathways for organic matter transformation over geological time, which resulted in production of compression fossils in the roof shale and fossilized-cuticle in the crevasse-splay, respectively. Fourier transform infrared spectroscopy methods are used to quantify functional groups, and the derived data are chemometrically evaluated. Results indicate that the compressions are, as anticipated, characterized in the crevasse-splay facies by a predominantly aromatic composition. The fossilized-cuticles, however, are mainly characterized by oxygen-containing aliphatics, confirming the influence of facies changes on preservation states of the species studied. Implications for preservation, taxonomy, and paleoecology are emphasized.