The subiculum is one of the major output structures of the hippocampal formation and is an important brain region for memory. We have previously reported that the subiculum of rodents can be morphologically divided into its temporal (ventral) two-thirds and the septal (dorsal) third and that the former can be further subdivided into the distal (Sub1) and proximal (Sub2) regions, on a basis of immunohistochemical localizations of several Sub2-specific proteins. However, it remains unclear whether detailed structural organization found in the temporal subiculum is applicable to the septal subiculum. In this study, we found that the distribution of fibronectin (FN1)-positive non-GABAergic, presumptive pyramidal cells exactly coincided with the extent of the Sub1 region of male mice. Using FN1 immunohistochemistry, the Sub1 was found to keep relatively constant size throughout the septotemporal axis of the subiculum. In contrast, the size of the Sub2 became smaller as it approached the septal side, and the Sub2 finally disappeared at the most septal level of the subiculum. Retrograde tracer experiments confirmed that FN1-positive Sub1 neurons projected to the retrosplenial cortex, which is thought to be associated with spatial memory, whereas FN1-negative Sub2 neurons projected to the nucleus accumbens associated with emotional memory. Considering both the functional segregation of these two subicular targets and the relative abundance of the Sub2 on the temporal side, the subiculum can be one of the neural substrates for functional differences between the septal and temporal hippocampal formation associated with the spatial and emotional memory, respectively.