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The brine shrimp <i>Artemia</i> has a ZW sex determination system with ZW chromosomes in females and ZZ chromosomes in males. <i>Artemia</i> has been considered a promising model organism for ZW sex-determining systems, but the genes involved in sex determination and differentiation of <i>Artemia</i> have not yet been identified. Here, we conducted transcriptome sequencing of female and male <i>A. franciscana</i> using PacBio Iso-Seq and Illumina RNA-Seq techniques to identify candidate sex determination genes. Among the 42,566 transcripts obtained from Iso-Seq, 23,514 were analyzed. Of these, 2065 (8.8%) were female specific, 2513 (10.7%) were male specific, and 18,936 (80.5%) were co-expressed in females and males. Based on GO enrichment analysis and expression values, we found 10 female-biased and 29 male-biased expressed genes, including <i>DMRT1</i> and <i>Sad</i> genes showing male-biased expression. Our results showed that <i>DMRT1</i> has three isoforms with five exons, while <i>Sad</i> has seven isoforms with 2–11 exons. The <i>Sad</i> gene is involved in ecdysteroid signaling related to molting and metamorphosis in arthropods. Further studies on ecdysteroid biosynthetic genes are needed to improve our understanding of <i>Artemia</i> sex determination. This study will provide a valuable resource for sex determination and differentiation studies on <i>Artemia</i> and other crustaceans with ZW systems.