Phosphorylation plays an important role in cellular signal transduction. Current phosphorylation-related databases often focus on the phosphorylation sites, which are mainly determined by mass spectrometry. Here, we present PhosphoNetworks, a phosphorylation database built on a high-resolution map of phosphorylation networks. This high-resolution map of phosphorylation networks provides not only the kinase-substrate relationships (KSRs), but also the specific phosphorylation sites on which the kinases act on the substrates. The database contains the most comprehensive dataset for KSRs, including the relationships from a recent high-throughput project for identification of KSRs using protein microarrays, as well as known KSRs curated from the literature. In addition, the database also includes several analytical tools for dissecting phosphorylation networks. PhosphoNetworks is expected to play a prominent role in proteomics and phosphorylation-related disease research.