Carbon and oxygen isotope compositions of the needle fibre calcite (NFC) from two soils observed in quarries (Villiers and Savagnier) in the Swiss Jura Mountains are used to investigate the processes involved in the formation of these calcite crystals in pedogenic environments. NFC occurs in soils with different macroscopic and microscopic morphologies. Three groups of microscopic morphologies are distinguished: simple needles (SN), simple needles with overgrowths (SNO), and simple needles with nanofibres (SNN), nanofibres being either organic or mineral in nature. These groups correspond to different stages in the formation and evolution of NFC. Evaluation of the delta C-13 and delta O-18 values of NFC and late calcite cements (LCC) in relationship to the composition of the carbonate host rock (CHR), and delta C-13(DIC) from the soil waters, indicate that both NFC and LCC are precipitated in isotopic equilibrium with the soil waters. Similar delta C-13 and delta O-18 values of the elongated NFC and the rhombohedral calcite crystals of the LCC suggest that the precipitation of these different calcite habits is not due to changes in physicochemical conditions. The growth of NFC crystals inside an organic mould formed by the fungal hyphae could explain the formation of calcite crystals in the shape of a needle in isotopic equilibrium with the local environment. The comparison of the delta C-13 and delta O-18 signatures of the various NFC morphological groups suggests that they likely evolve in the soil solution from calcite crystals liberated during the degradation of fungal hyphae walls. The NFC may be a proxy of the soil conditions (temperature and vegetation) during its precipitation, and also an indicator of biogenic (fungal) activity.