In order to investigate the relationship between NAC domain transcription factors and developmental lignification of peach endocarp, two NAC domain transcription factor genes PpNST1 and PpSND1 were isolated from peach (Prunus persica L. ‘Okubo’) endocarp by homologous cloning. Sequence analysis indicated that both PpNST1 and PpSND1 were 1 188 bp, encoding 396 amino acids. The predicted proteins of them contained one NAC domain in N terminus and two featured domains (LP-box and WQ-box) in C terminus. Phylogenetic analysis results revealed that PpNST1 and PpSND1 were closely related to secondary cell wall formation- and lignification-related NAC domain transcription factors in Malus domestica, Vitis vinifera, Populus trichocarpa and Arabidopsis thaliana. Quantitative real-time PCR analysis showed that the expression patterns of PpNST1 and PpSND1 were dramatically up-regulated during the lignification of peach endocarp, and their transcript expression levels were more abundant in endocarp than in mesocarp. Moreover, the expression analysis of the putative downstream targets of PpNST1 and PpSND1 suggested that they might play important role in endocarp developmental lignification.