The common Chinese cuttlefish (Sepiella japonica) is active, resourceful cephalopod species with a rich nutrition and medicinal value. However, artificial hatching is currently challenged by low survival rate of larvae due to abnormal embryonic development. To date, less is investigated about the transcriptome during embryogenesis of cuttlefish. In this study, embryos of S. japonica from eye primordium formation to larval growing stage were collected and used for RNA-Seq analysis.</p><p>In the embryonic development process, the morphological changes of the eyes were relatively obvious. In addition, eye lesions were obvious when infected with streptococcus. Therefore, in here, we carried out a transcriptome sequencing on S. japonica embryos from eye primordium formation to larvae growing by RNA-Seq. Digital gene expression (DGE) analysis among three development stages was performed to identify of key genes and pathways that are involved in the regulation of embryo development.