In the present study, the mechanism of jarosite biosynthesis mediated by extracellular polymer substances (EPSs) of Purpureocillium lilacinum strain Y3 at gene level was investigated. Yellow-ocher jarosite minerals covered mycelia pellets entirely within 72h, corresponding to a reduction of Fe3+ of 70.9% in the biomineralization process induced by P. lilacinum Y3. The maximum biomass accumulation reached to 12.9 g/L in pure culture, 2.8 g/L with only 0.02M Fe3+ addition, and 6.4 g/L with both 0.02M Fe3+ and 0.1M K+ addition, respectively, indicating that jarosite biosynthesis largely alleviated the inhibition of Fe3+ to the fungal strain. Thereafter, the analysis of EPSs compositions suggested that protein content was affected more evidently than polysaccharides in the biomineralization system. Furthermore, real time quantitative PCR assays revealed that signal transduction genes and abundance of membrane transporters were activated quickly in responding to the stimulation of Fe3+ and fungus-mineral interactions. Then, the expression of adhesive proteins and extracellular proteins was highly up-regulated to facilitate the formation of jarosite minerals on the cell surface. Finally, X-ray photoelectron spectroscopy analysis supported that amine, carboxyl, phosphate groups present on the mycelia provided Fe3+ and K+ binding sites for biosynthesis of jarosite.