Abstract Background Nickel hyperaccumulator plants are of much interest for their evolution and unique ecophysiology, and also for potential applications in agromining—a novel technology that uses plants to extract valuable metals from soil. The majority of nickel hyperaccumulators are known from ultramafic soils in tropical regions (Cuba, New Caledonia and Southeast Asia), and one genus, Phyllanthus (Phyllanthaceae), is globally the most represented taxonomic entity. A number of tropical Phyllanthus-species have the potential to be used as ‘metal crops’ in agromining operations mainly because of their ease in cultivation and their ability to attain high nickel concentrations and biomass yields. Results One of the most promising species globally for agromining, is the here newly described species Phyllanthus rufuschaneyi. This species can be classified in subgenus Gomphidium on account of its staminate nectar disc and pistillate entire style and represents the most western species of this diverse group. The flower structure indicates that this species is probably pollinated by Epicephala moths. Conclusions Phyllanthus rufuschaneyi is an extremely rare taxon in the wild, restricted to Lompoyou Hill near Kinabalu Park in Sabah, Malaysia. Its utilization in agromining will be a mechanism for conservation of the taxon, and highlights the importance of habitat and germplasm preservation if rare species are to be used in novel green technologies.