The recovery of precious metals is a project with both economic and environmental significance. In this paper, it presents how to use bacterial mineralization to selectively recover gold from multi-ionic aqueous systems. The Bacillus licheniformis FZUL-63, separated from a landscape lake in FuZhou University, was shown to selectively mineralize and precipitate gold from coexisting ions in aqueous solution. The removal of Au(III) was almost happened in first hour, and FTIR data show that the amino, carboxyl and phosphate groups on the surface of the bacteria are related to the adsorption of gold ions. XPS results implied that Au(III) ions are reduced to monovalent, and then the Au(I) was adsorbed on the bacterial surface at the beginning stage(first hour). XRD results showed the gold biomineralization began about 10 hours after the interaction between Au(III) ions and bacteria. The Au(III) mineralization has been rarely influenced by other co-existing metal ions. TEM analysis shows the gold nanoparticles are polyhedral structure with a particle size of ~20 nm. The Bacillus licheniformis FZUL-63 could selectively mineralize and recover 478 mg/g(dry biomass) gold from aqua regia-based metal wastewater through four cycles. It could be of great potential in the practical application.