Distant hybridization is widely applied in genetic improvement of aquatic animals. Although this technique should be suitable for genetic improvement of grouper, few studies related to offspring produced via distant hybridization have been reported. There we studied the gene expression dynamics of early embryonic development of groupers from self-breeding, intraspecific breeding and intergeneric hybridization. We first obtained offspring from female brown-marbled grouper (Epinephelus fuscoguttatus) and male leopard coral grouper (Plectropomus leopardus) and described the morphological characteristics of different developmental stages of embryos. We then constructed the transcriptome maps during early embryonic development of hybrid groupers. In addition, we also found that the process of MZT occurred from high blastula to early gastrula stage in the embryo of hybrid grouper and that wnt signaling pathway play an important role in dorsal-ventral axial formation during embryonic development of grouper. These results provide a foundation for the hybrid breeding of leopard coral grouper.