Mice deficient in transcription factor gene Emx2 show developmental alterations in the hippocampal dentate gyrus. Emx2, however, is also expressed in the region around the developing hippocampal fissure. The developing fissure contains a radial glial scaffolding, and is surrounded by the outer marginal zone and the dentate marginal zone, which become specifically colonized by neurons and differentiate into stratum lacunosum-moleculare and molecular layer of the dentate, respectively. In this study we show that the Emx2 mutant lacks the glial scaffolding of the fissure and has an outer marginal zone (precursor of the stratum lacunosum-moleculare), as well as a dentate marginal zone severely reduced in size while most of the reelin (Reln)-expressing cells that should occupy it fail to be generated. We have also identified a subpopulation of hippocampal Reln-expressing cells of the marginal zone, probably born in the hem, expressing a specific combination of markers, and for which Emx2 is not essentially required. Additionally, we show differential mutant phenotypes of both Emx2 and Pax6 in neocortical vs. hippocampal Reln-expressing cells, indicating differential development of both subpopulations.