Abstract: Artemia is not only one of the most important live feed for larvi culture, but also an ideal experimental organism for scientific research. Female Artemia produce either nauplii via ovoviviparous pathway or diapause cyst via oviparous pathway. In order to reveal the mechanism of different reproductive modes of Artemia, the reproductive differential transcriptomes of parthenogenetic Artemia were constructed, bioinformatics analysis were performed to screen reproductive differential expression genes, and the gene expression patterns were studied by using qRT-PCR. Transcriptome analysis showed that there were 1452 differentially expressed genes, of which 601 genes were up-regulated and 851 down-regulated in the abscising carpopodium. According to GO function classification, 1243306 and 530 unigene were annotated into biological process, cell composition and molecular function respectively. KEGG enrichment analysis showed that differential genes were significantly enriched in antigen processing and ribosome pathways. Combined with transcriptome data and qRT-PCR analysis, six reproductive-related genes were screened and verified. The results showed that all the six reproductive-related genes had higher expression in oviparous Artemia than in ovoviviparous Artemia. In addition, the conserved domains of the proteins encoded by six candidate reproductive related genes were predicted and phylogenetic trees were constructed respectively. The results showed that the protein domains were consistent with the previously reported reproductive genes. Over all, our study indicated that the selected six genes may influence the reproductive process of Artemia. This study provides valuable information for dissecting the molecular mechanism of reproductive pattern in the parthenogenetic Artemia, and may also help to refine the reproductive biological theory of Artemia.