This study describes the yeast Rhodotorula mucilaginosa strain LM9 isolated from copper-bearing, organic-rich Kupferschiefer black shale and its role in copper biotransformation. Strain LM9 exhibited great ability to simultaneously mobilize and immobilize copper from this sedimentary rock. In addition, it showed considerable resistance to copper and high uptake of this metal. Moreover, malic and oxalic acid as well as siderophore (rhodotorulic acid) produced by this strain enhanced its resistance by promoting the mobilization and complexation of copper from black shale. These processes, characterized here under laboratory conditions, are assumed to play a role in copper cycling in black shale as well as in the adaptation of strain LM9 to the conditions prevailing in its natural mine habitat. The findings of this study indicate that yeast strain LM9 might be used for the recovery of copper particularly from alkaline or slightly neutral ores in a non-chemical environmentally-friendly procedure.