Bioleaching of Cu and Fe in low-grade chalcopyrite using Penicillium janthinellum strian GXCR was studied. As a result, shaking bioleaching was more efficient than submerged bioleaching; Cu bioleaching was much better than Fe bioleaching; under conditions of optimum carbon source (10% sucrose, W/V), optimum nitrogen source (1.5% NaNO3, W/V), shaking bioleaching and the optimum combination of conditions (initial pH 6.0 in leaching media, 5% (W/V) 200-mesh ore and initial inocula of 3.0x10(5) conidia/mL), Cu bioleaching efficiency reached 87.31% (W/W). One of the most important factors affecting Cu bioleaching in shaking bioleaching was the initial pH in leaching media (F > F0.05). The major organic acids for Cu and Fe bioleaching were citric and oxalic acids, respectively. Low bioleaching efficiency by submerged bioleaching was due to low production of citric and oxalic acids. The mechanisms employed by the GXCR in Cu bioleaching included biochemical functions of citric and oxalic acids as well as ore crack caused by mechanical power generated from mycelial growth.