Genomic and post-genomic research is responsible for the accumulation of enormous data, which allows the formation of whole views of the organisms under investigation. Genome research on pathogenic and associative bacteria is providing important information on bacteria–plant interactions, especially on type-Ⅲ secretion systems (TTSS) and their role in the interaction of bacteria with plants. In the present paper , we summarized plant-associated bacterial genome research on bacteria–plant interactions in details. Trends in future research have also been analyzed.