Receptor-type protein tyrosine phosphatase zeta/beta (RPTPzeta) is a transmembrane chondroitin sulfate proteoglycan (CSPG) and has been shown to play crucial roles in controlling axonal growth and neuronal migration. The RPTPzeta has two transmembranous isoforms, shorter receptor form of RPTPzeta (sRPTPzeta) and full-length receptor form of RPTPzeta (fRPTPzeta), but no studies have been reported about functional difference of these two isoforms. In the present study, therefore, we examined whether or not two RPTPzeta isoforms have different role in controlling dendritic morphology and synaptic number in cultured hippocampal neurons using the quantitative morphometrical analysis. Confocal microscopic observation showed that the immunoreactivity of RPTPzeta was observed throughout cells such as axons, growth cones, and dendrites at the early stages of neuronal culture, while it was seen predominantly on dendrites at the late stages. Western blotting analysis revealed that fRPTPzeta was mainly expressed at the early stages of culture and both RPTPzeta isoforms were expressed at late stages of culture. The overexpression of sRPTPzeta in hippocampal neurons increased the dendritic arborization without altering the average length of dendritic branches, whereas that of fRPTPzeta decreased the dendritic arborization and increased the average length of dendritic branches. The RNA interference of fRPTPzeta expression increased the dendritic arborization without altering the average length of dendritic branches. The overexpression of fRPTPzeta decreased the density of hippocampal dendritic synapses, but that of sRPTPzeta had no effects. Pleiotrophin, a ligand for RPTPzeta to interfere the phosphatase activity, increased the density of hippocampal dendritic synapses. Thus, the present study demonstrates that two transmembranous RPTPzeta isoforms have different functions for regulating dendritogenesis and synaptogenesis.