Caffeoyl shikimate esterase (CSE) is a key enzyme in lignin synthesis in Arabidopsis thaliana. To determine the role of CSE in lignification of the endocarp in peach (Prunus persica L.) fruit, we cloned and characterized the P. persica CSE homolog, which we designated PpCSE. The 954 - bp PpCSE gene encoded a 317 - amino acid polypeptide. PpCSE expression patterns in the mesocarp and endocarp changed during peach fruit development. There was no significant difference between the expression levels of PpCSE in the mesocarp and endocarp at 39 and 44 days after full bloom (DAFB), but the expression level of PpCSE in the endocarp at 50 and 55 DAFB was 80.73 and 72.75 times higher, respectively, than that in the mesocarp. During peach fruit development, PpCSE expression in the endocarp increased rapidly; the relative PpCSE expression level at 50 DAFB was 122.70 times higher than that at 39 DAFB. At the protein level, CSE was detected in the peach fruit endocarp at 50 and 55 DAFB. Our study suggests that PpCSE expression during peach fruit development is closely related to the degree of endocarp lignification.