The 2009 Cold Spring Harbor Conference on Plant Genomes is the seventh in a series of biennial scientific conferences on plant genomes. The meeting will focus on functional and evolutionary genomics in a diverse range of plants, and will explore themes and technologies from other genomes, including those of animals and fungi. The conference is intended to provide a forum at which to review progress in genome analysis of the major plant groups and to determine the similarities and differences in genome structure, composition, and function of the major groups of experimental and crop plants. A key feature of the seventh meeting is the explicit focus on genes, networks, and applications. The conference will include a diverse array of topics including sessions on (1) celebrating the maize genome; 2) hybrids and heterosis; 3) genomes, plants and microbes; 4) innovative phenotyping; 5) integrating omics/iPlant; 6) models; and 7) evolution inside and outside the lab. Keynote talks will highlight progress on the 12 Drosophila genomes and transcriptional network evolution. Finally, a workshop will facilitate discussion of plant genomes and the progress towards the Arabidopsis 2010 goals. Attendance at this conference is expected to fall between 150 and 200 international scientists, including graduate students, postdoctoral workers, and principal investigators. The intellectual merits of this conference include the opportunity for investigators at all stages of their scientific careers to share and discuss their latest results and concepts. The informal peer review that occurs during both talks and poster sessions is invaluable, as it provides rapid feedback that can steer and accelerate future research. This conference also provides ample opportunity for learning and for building collaborations, as no sessions are held in parallel, and thus all attendees share a common experience, while the secluded venue maximizes the likelihood of productive scientific exchange. Several aspects of this conference have a particularly broad impact. One is the active participation of younger scientists, who particularly benefit from the opportunity to present their latest ideas. Another is the conference archive, which allows participants to share aspects of the conference with their colleagues who were unable to attend, while protecting the rights of authors who present unpublished research.