Novel ecosystem development is occurring within the western boreal forest of Canada due to land reclamation following oil sand surface mining. Sphagnum peat is the primary organic amendment used to reconstruct soil in these novel ecosystems. We hypothesised that ecosystem recovery would be indicated by an increasing similarity in the biomolecular characteristics of novel soil organic matter (SOM) derived from peat to those of natural boreal ecosystems. We evaluated the use of the homologous series of long chain (⩾ C21) n-alkanes with odd/even predominance to monitor the re-establishment of boreal forest on these anthropogenic soils. The lipids were extracted from dominant vegetation inputs and SOM from a series of natural and novel ecosystem reference plots. Twice the concentration of n-alkanes was extracted from natural than from novel ecosystem SOM (p < 0.01). We observed unique n-alkane signatures for the source vegetation, e.g. peat material was dominated by C31, and aspen (Populus tremuloides Michx.) leaves by C25. The n-alkane distribution differed between the two systems (p < 0.001) and reflected the dominant vegetation input, i.e. peat or tree species. Our results indicate that further research is required to clarify the influence of vegetation or disturbance on the signature of n-alkanes in SOM; however, the use of n-alkanes as biomarkers of novel ecosystem development is a promising application.