The Bacterial Isolate Genome Sequence Database (BIGSDB) is a scalable, open-source, web-accessible database system designed to store, retrieve, and analyze linked phenotypic and genotypic information for bacterial isolates. It integrates phenotype and sequence data, ranging from single sequence reads to whole genome data, enabling efficient linking for an unlimited number of bacterial specimens. BIGSDB builds on the mlstdbNet software, which is widely used for multilocus sequence typing (MLST) data storage and distribution, and incorporates the ability to define and identify any number of loci and genetic variants within stored nucleotide sequences. These loci can be organized into 'schemes' for isolate characterization or evolutionary and functional analyses. BIGSDB supports multiple names for isolates and loci, allowing cross-referencing of different studies and approaches. The software includes LIMS functionality for laboratory sample management and fine-grained authentication to enable community annotation. BIGSDB is demonstrated with applications to the genera *Neisseria* and *Streptococcus*, showcasing its utility in population genomics research. The source code and documentation are available at http://pubmlst.org/software/database/bigsdb/.The Bacterial Isolate Genome Sequence Database (BIGSDB) is a scalable, open-source, web-accessible database system designed to store, retrieve, and analyze linked phenotypic and genotypic information for bacterial isolates. It integrates phenotype and sequence data, ranging from single sequence reads to whole genome data, enabling efficient linking for an unlimited number of bacterial specimens. BIGSDB builds on the mlstdbNet software, which is widely used for multilocus sequence typing (MLST) data storage and distribution, and incorporates the ability to define and identify any number of loci and genetic variants within stored nucleotide sequences. These loci can be organized into 'schemes' for isolate characterization or evolutionary and functional analyses. BIGSDB supports multiple names for isolates and loci, allowing cross-referencing of different studies and approaches. The software includes LIMS functionality for laboratory sample management and fine-grained authentication to enable community annotation. BIGSDB is demonstrated with applications to the genera *Neisseria* and *Streptococcus*, showcasing its utility in population genomics research. The source code and documentation are available at http://pubmlst.org/software/database/bigsdb/.