Raman spectroscopy is a minimally intrusive and minimally destructive technique that has played an important role in analyzing Precambrian carbonaceous microfossils and microstructures. Previous studies have shown that heterogeneities in structural order of carbonaceous material (CM) as revealed by Raman spectroscopy can be preserved in Proterozoic silicified cyanobacterial fossils. However, such heterogeneities have not been documented in Proterozoic eukaryotic microfossils preserved as carbonaceous compressions. In this study, we used Raman spectroscopy to investigate the structural characteristics of organic-walled microfossils, including eukaryotes preserved as carbonaceous compressions, from the late Paleoproterozoic Ruyang Group and the early Neoproterozoic (Tonian) Liulaobei Formation in the North China Craton. Raman geothermometers indicate that CM experienced low-grade metamorphism with apparent peak metamorphic temperatures of similar to 200 degrees C for both the Ruyang and Liulaobei microfossils. Heterogeneities in structural characteristics of CM in eukaryotic microfossils were found among different subcellular structures of Shuiyousphaeridium macroreticulatum and among different taxa from the same stratigraphic horizon. We suggest that these heterogeneities can be attributed to differences in precursor organic compounds; thus, the importance of organic precursors should be considered in CM Raman geothermometry studies, especially in environments where heating events occurred quickly. The Raman data presented here are also consistent with hypotheses that the Ruyang microfossils Dictyosphaera delicata and S. macroreticulatum are biologically conspecific taxa with their vesicle walls having similar CM Raman features, and that the Liulaobei microfossils Leiosphaeridia jacutica and L. tenuissima are distinct taxa despite their similarities in morphologies other than vesicle wall thickness. Although more data are needed to verify the consistency of interspecies, intraspecies, and intraspecimen variability, this study indicates that Raman spectroscopy may have the potential to provide an independent test of early eukaryote taxonomy, which has been traditionally based only on morphological features, and to reveal heterogeneities of CM of early eukaryotic organisms.