The Dendrome project provides custom informatics tools and databases to manage the flood of information resulting from high-throughput genomics projects in forest trees from sample collection to downstream analysis. This resource is further enhanced with systems that are well connected with federated databases, automated data flows, standardized annotations and quality control processes. A sample tracking system sits at the forefront of most large-scale projects. Barcode identifiers assigned during sample collection are maintained in the database to identify a tree through DNA extraction, resequencing, genotyping and phenotyping. The supporting TreeGenes database contains ten curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools. TreeGenes has been expanded to hold genomic and transcriptomic databases through the GBrowse interface. Annotated transcriptomic studies resulting from next-generation sequencing are now available for 13 conifer species. DiversiTree, an extensive user-friendly desktop-style interface, queries the TreeGenes database and is designed for bulk retrieval of Sanger resequencing data. It provides the community with access to a multitude of data types including ESTs, primers, tracefiles, SNPs, individual tree data, genotypes and phenotypes. The variety of outputs available allows users to perform high-resolution dissection of traits and relate molecular diversity to functional variation. Recent development has focused on web services to connect geo-referenced individuals with important ecological and physiological databases as well as the development of ontologies to enhance comparative capabilities. The combined resources of the Dendrome project serve as a powerful knowledge environment for genotype-phenotype information resulting from a multitude of large-scale genomics projects.