Insularity, geological history and biogeography have made from New-Caledonia a hot spot of biodiversity where extremely diversified ecosystems occupies ultramafic terrains with drastic edaphic conditions in terms of fertility and metallic toxicity. In the framework of the mine project of the Koniambo Massif, a large nickel deposit, we tried to explore the diversity of ectomycorrhizal symbioses within these poorly explored natural ultramafic ecosystems. Floristic inventories along an altitudinal gradient ranging from 700 to 900 m evidenced 4 different plant communities. The 2 lower plant communities, 3 and 4, were dominated by 2 endemic tree genera, Tristaniopsis (Leptospermoideae) and Nothofagus (Nothofagaceae) respectively, whose ectomycorrhizal (ECM) status was shown and explored through molecular methods on sporocarps, mycorrhizae and soil mycelium. We evidenced a diversified fungal community in the basal plant community dominated by two tree species of the genus Nothofagus. The molecular characterization of these ECM fungi was established on the total ribosomal inter transcribed spacer (ITS) by PCR-sequencing and BLASTn analysis, revealing the relative abundance of the Cortinariaceae among our samples. Samples belonging to this fungal family were phylogenetically analyzed on the same ITS, in reference to sequences of samples with geographically different origins, including countries derived from the Gondwanaland fragmentation. If no clear phylogenetical relationships were evidenced, our study confirmed the same relative dominance of ECM Nothofagaceae, as well as the relative abundance of associated Cortinariaceae, in New Caledonia as in several of the Gondwanaland-originating countries.