Purpose: To assess the effect of incorporation of 5 wt% nano-hydroxyapatite particles (Nano-HAp) on the ultra-morphological characteristics of sound and caries-affected dentin substrate/ conventional glass ionomer cement (CGIC) and resin-modified glass ionomer cement (RMGIC) interfaces. Materials and Methods: Occlusal surfaces of 16 extracted permanent human caries-free molars were ground to expose flat dentin surfaces. Half of the specimens (n=8) were subjected to pH-cycling to create artificial caries-affected dentin. Specimens were randomly restored with one of the tested restorative materials either control (CGIC and RMGIC) or experimental (CGIC and RMGIC modified with Nano-HAp). Different restorative materials were mixed according to manufacturer instructions and then built-up on the sound or caries-affected dentin surfaces. All specimens were stored in artificial saliva either for 24 hours or 9 months. Specimens were then prepared and observed under field emission scanning electron microscope (FESEM) for ultra-morphological evaluation of dentin-restoration interfaces. Results: FESEM observations showed no marked ultra-morphological changes in Nano-HAp modified groups/ dentin interfaces in compared to control groups. There was significant increase in microcracks and pores within the matrix of all GIC groups. Moreover, there were multiples microcracks extended all over the restorations matrix with microgaps formation at dentin-restoration interfaces for all caries-affected dentin and 9 months aging period groups. Conclusion: The unique properties of glass ionomer cements were greatly diminished with bonding to caries-affected dentin and gradually declined with aging process. While there was no additional effect was observed from addition of Nano-HAp to these tested cements regarding their ultra-morphological characteristics features under FESEM.