• 12 C and 13 C isotope abundance in S. annotinum has been investigated for the first time. • δ 13 C value in S. annotinum is lower than that reported in other C 3 plants. • Different above- and below-ground S. annotinum organs have distinct δ 13 C values. • δ 13 C values of S. annotinum are connected with local plant diversity. Physiological processes in plants and plant–environment interactions can be analysed from the composition of stable carbon isotopes ( 13 C/ 12 C). This ratio can be indicated using the δ (delta) notation. Substantial evidence has been published in recent years demonstrating that post-photosynthetic fractionation occurs in plants and leads to differences in 13 C-enrichment in heterotrophic (as compared with autotrophic) organs. Yet our understanding of processes leading to 13 C divergence between leaves and heterotrophic tissues remains low. Large part of the isotope analysis is concerned with angiosperms, but not spore-bearing tracheophytes. In this study, we explored the 12 C and 13 C isotope distribution in above-ground and below-ground organs of an archaic lycophyte Spinulum annotinum (L.) A.Haines (interrupted clubmoss). The main objectives of this study were to determine the natural distribution of stable carbon isotopes in sporophytes of S. annotinum and to discuss possible causes for differences in δ 13 C. The study revealed that there are significant differences between δ 13 C in different S. annotinum organs. The δ 13 C values varied by about 2.4‰. The highest δ 13 C values were −30.0‰ in roots and the lowest were −32.4‰ in plagiotropic shoot leaves. The distance to a body of water had no significant effect on δ 13 C values in S. annotinum . Outgrowth size did not have a clear relationship with δ 13 C in S. annotinum . The Shannon Diversity Index was a significant predictor for δ 13 C values in S. annotinum . The uncovered δ 13 C and the relationship with abiotic habitat conditions and neighbouring plant species in the community provide a base for future lycophyte ecophysiology research.