This study examined the ultrastructure of both intact and caries affected dentin-adhesive interface after artificial secondary caries formation, using scanning electron microscopy and nanoindentation testing. Half of the prepared specimens were bonded with Clearfil SE Bond (Kuraray Medical, Japan) and a resin composite (Metafil Flo, Sun Medical, Japan) for the nanoindentation test. The other specimens were stored in a buffered demineralizing solution for 90 minutes, then observed using SEM. An acid-base resistant zone (ABRZ) was observed beneath the hybrid layer, distinguished by argon-ion etching. The ABRZ of caries-affected dentin was thicker than that of normal dentin, while its nanohardess was lower than normal dentin (p<0.05). It is suggested that the monomer of Clearfil SE Bond penetrated deeper than previously reported, creating a so-called "hybrid layer." However, its physical properties depended on the condition of the dentin.