Iron acquisition represents a challenging problem for bacteria because Fe is an essential element with very low bioavailability. Siderophores, produced by microorganisms, are high-affinity ferric iron chelators with attractive structural diversity. Two main pathways for siderophore biosynthesis have been reported. One involves multifunctional metasynthase nonribosomal peptide synthetase (NRPS), while the other is NRPS-independent (NIS) and catalyzed by siderophore synthetase superfamily. Biosynthesis of siderophores has been the focus of inquiry for nearly twenty years. The enzymology of NRPS-mediated biosynthetic pathway of siderophore has been intensively studied and a vast knowledge of the NRPS-independent siderophore (NIS) biosynthesis is increasing. As siderophore is one type of the important secondary metabolites from actinomycetes, genetic and biochemical studies of its biosynthetic pathways will provide an opportunity to develop potential antibacterial agents, and enable the increasing understanding of the biosynthetic mechanism of this kind of natural products as well. Here we summarize the recent progress in mechanism of siderophore biosynthesis.