Spatial tuning of pyramidal cells has been observed in diverse neocortical regions, but a systematic characterization of the properties of spatially tuned neurons across cortical layers and regions is lacking. Using mice navigating through virtual environments, we find topographical organizational principles for the representation of spatial features in the medial prefrontal cortex. We show that spatial tuning emerges across layers with a dorso-ventral gradient in the depth of spatial tuning, which resides in superficial layers. Moreover, the prefrontal cortex shows hemispheric lateralization of spatial tuning such that neurons located in the left hemisphere display more pronounced spatial tuning. During exploration of a novel compared to a familiar context, a different picture emerges. Context discrimination and familiarity detection is higher in superficial compared to deep layers. However, neurons of the right medial prefrontal cortex discriminate more efficiently between contexts than cells in the left hemisphere. Jointly, these results reveal a complex topographic organization of spatial representation and suggest a division of labor among prefrontal layers and subregions in the encoding of spatial position in the current environment and context discrimination.