Large genomic DNA insert-containing libraries e.g. bacterial artificial chromosome (BAC) libraries have made great contributions to advanced genomic studies, such as genome-wide sequencing, syntenic analysis between genomes, physical mapping, and positional cloning of important QTL genes in soybean or other legume. As recent advances in next-generation sequencing (NGS) technology, application of BAC or other large insert-containing library has become less demanding. We briefly review the history and applications of soybean BAC library technology. The challenge and future prospective of soybean BAC library technology in the post genomic-era are also discussed.