The crustacean Daphnia magna produces females parthenogenetically under healthy conditions. In response to environmental stresses such as starvation and higher population density, it produces males that are genetically identical to their sisters. Environment-dependent male production in D. magna can be interpreted as the shift of the position of the sex on the spectrum from the female-side to the male-side by the environmental cues. We previously had identified that the evolutionary conserved sex-determining gene Doublesex1 (Dsx1) implements the male developmental program in D. magna. We also had reported regulatory factors including the lncRNA DAPALR for Dsx1 expression. However, little is still known about the role of sexually differential expression of gene isoforms and the other lncRNAs on the establishment of the binary sex in D. magna. To identify sex-specific mRNA isoforms and lncRNAs, we aim to perform full-length RNA-Sequencing (Iso-Seq) and the short-read Illumina RNA-Seq on the male and female embryos at 40 hours post ovulation that shows sexually dimorphic expression of Dsx1. After combining the long-read data and obtained unique full-length isoforms, we will map RNA-Seq data to the obtained transcriptome to quantify differential isoform usage between males and females. This analysis may provide a comprehensive evaluation of isoform usage between genetically identical males and females, revealing that differential isoform usage is important for sex determination and differentiation.