Many studies have described structural and functional heterogeneity across the hippocampus, but different fields of neuroscience (behavioral, anatomical, and gene expression studies) have produced disparate views of hippocampal organization. To help bridge the gaps between these data, we analyzed and mapped mouse gene expression patterns across the entire hippocampus and subiculum to create a comprehensive Hippocampus Gene Expression Atlas (HGEA) with 20 distinct molecular subregions. Guided by the HGEA, we traced the anatomical inputs and outputs of each HGEA subregion to create the most detailed wiring diagram of the hippocampus to date. Finally, hippocampal network analysis revealed that the hippocampus is a multiscale hierarchical network that contributes to separate brain-wide networks hypothesized to influence spatial navigation, social, and homeostatic behaviors. Overall, the HGEA provides a foundational roadmap that integrates gene expression and connectivity for the future genetic dissection of hippocampal cell types in behavior and how these cell types are impacted by neurological diseases, like Alzheimer’s disease.