Hatching enzyme (HE) is the most critical enzyme in the process of fish hatching. Pikeperch, Sander lucioperca, is one of economical and ferocious fish with long embryonic incubation and its long and irregular hatching time easily leads to the decrease of its fingerlings due to cannibalism. HE is one of the most important factors that affect the membrane effusion of fish eggs during incubation. The present study aimed to clone HE genes and to reveal the HE expression patterns of pikeperch during its hatching process. In this study, the full-length cDNAs of high choriolytic enzyme gene (HCE) and low choriolytic enzyme gene (LCE) from pikeperch were cloned and their expressions were performed using qRT-PCR and in situ hybridization. The results showed that the full-length cDNAs of HCE and LCE were comprised of 1189 bp and 1147 bp, respectively, and the open reading frames (ORFs) obtained were 876 bp and 798 bp, encoded proteins of 291 and 265 amino acids, respectively. Phylogenetic analysis showed high homology of HE in Percidae, far from amphibians, birds, and insects. HE genes maintained high expression from body segment appearance stage to hatching stage, and low expression in early embryo and larval stage of pikeperch. HE transcripts were initially detectable at body segment appearance stage in the head region and on the surface of the yolk sac. At hatching stage, strong staining was observed in the whole body from head to the tail. Compared with other fishes, the special spatiotemporal expression pattern of hatching enzyme may be the key factor leading to the irregular hatching time of pikeperch. Our study might enhance our understanding of the hatching mechanism of pikeperch. [ABSTRACT FROM AUTHOR]