Abstract Background and aims Most studies of the relationships between the composition of soil organic matter and plant cover have been carried out at the plant genera level. However, they have largely overlooked the potential effects that plant varieties, belonging to the same genus, can have on soil organic matter. Methods We investigated whether plant varieties belonging to different Salix species (S. dasyclados and S. viminalis) impacted the composition of organic matter using mid-infrared spectroscopy and pyrolysis GC/MS. Top-soils were taken from an 18 year-old long-term field trial where six Salix varieties were grown as short-rotation coppice under two fertilisation regimes. Results Significant differences in the molecular composition and diversity of the soil organic matter were observed in the fertilised plots. The effects were mostly visible at the species level, i.e. the organic matter in soil under S. dasyclados varieties had higher molecular diversity and lignin content than under S. viminalis, potentially due to differences in the amount and composition of their litter inputs. Smaller differences among varieties from the same species were also observed. No significant effects of Salix varieties were observed in the unfertilised plots. The relatively high degree of spatial variability of several soil properties found in these plots may have masked plant variety and/or species effects. Conclusion This study provides evidence that the identity of Salix species or varieties can affect the molecular composition and diversity of soil organic matter. The corresponding traits should be considered in breeding programmes to enhance soil organic C accumulation and persistence.