Perpendicular recording media, where the recording layer is deposited on carbon-based synthetic nucleation (SN) layers, have been investigated for magnetic and microstructural properties. It was observed that the recording layers deposited directly on low-pressure sputtered Ru layers with and without an SN layer showed a similar microstructure from plan-view TEM images. However, the magnetic properties of the media with SN layer show better intergranular segregation, whereas the media without SN layer show signs of strong intergranular exchange coupling. Recording layer thickness dependent studies indicate that the 3-nm-thick recording layer deposited on the Ru layer directly without SN layer showed rectangular hysteresis loop, indicating the formation of a continuous layer. A recording layer (3 nm) deposited on an SN layer showed a superparamagnetic type of hysteresis loop, indicating better intergranular segregation. Transmission electron microscopy observations also indicate that the recording layer deposited on SN layer shows better segregated structure even at 3 nm. The results indicate that SN layer is beneficial for grain size reduction as well as eliminating the initial continuous layer formed in the recording layer.