Glutamatergic mossy cells (MCs) are responsible for the associational and commissural connectivity of the dentate gyrus. MCs are widely distributed along the dorsoventral axis, but potential heterogeneity within MCs is scarcely explored. Here, we showed that MCs consist of two subpopulations which differ in their neuronal properties and functions. We discovered that MCs, depending on their dorsoventral location, extend distinct axonal projections in the molecular layers. Comparative transcriptional profiling of dorsal and ventral MCs revealed different neurobiological characteristics in axon guidance and synapse assembly. Despite common activation by external stimuli, dorsal MCs, but not ventral MCs, provide net inhibitory control on granule cells across the longitudinal axis. Furthermore, dorsal MC inhibition, unlikely that of ventral MCs, increases behavioral anxiety and disables rapid contextual discrimination. Collectively, dorsoventral heterogeneity of MCs may provide a novel mechanism for functional differentiation as well as distinct association along the longitudinal extent of the hippocampus.