The HGTree database provides putative genome-wide horizontal gene transfer (HGT) information for 2,472 completely sequenced prokaryotic genomes. HGT detection is based on an explicit evolutionary model of tree reconstruction and relies on evaluating the conflicts between phylogenetic tree of each orthologous gene set and corresponding 16S rRNA species tree. The database provides quick and easy access to HGT-related genes in hundreds of prokaryotic genomes and provides functionalities to detect HGT in user-customized datasets and gene and genome sequences. The database is freely available and can be easily scaled and updated to keep pace with the rapid rise in genomic information.