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Jellyfish is a common toxic zooplankton in ocean. We successfully captured a kind of jellyfish 200 m underwater in Antarctica, and identified it as a jellyfish Cyanea sp. through morphological examination and MT-CO1 phylogenetic analysis. A total of 40,468 unigenes were harvested through transcriptome sequencing. We also successfully annotated 12,955 (32.01%) unigenes with the NR database, 10,882 (26.89%) unigenes with the SWISSPROT database, 4951 (12.23%) unigenes with the GO database, and 4901 (12.11%) unigenes with the KEGG database. In the proteomic analysis, a total of 11,159 peptides and 2630 proteins were harvested using the constructed transcriptome as the database. A number of 771 (29.31%) and 841 (31.98%) proteins were annotated against the GO and KEGG database, respectively. Moreover, a number of 29 toxic proteins matched from the 145 toxin-related unigenes were successfully screened, including 6 metalloproteinases, 4 phospholipases, 2 serine proteases, 1 serine protease inhibitor, 7 toxin-related venom and 9 other toxins. Our study is the first to identify a polar jellyfish Cyanea sp. with transcriptomics and proteomics, and these data can further serve as a public database for the identification of potential polar jellyfish-derived lead compounds feasibly functioning in the cold environment. With increasing discussions on marine biodiversity and global warming, polar species have gradually become a focus for research. To the best of our knowledge, there is only one paper in pubMed about the mitochondrial genome of the Antarctic stalked jellyfish Haliclystus antarcticus Pfeffer. In this study, we captured a type of jellyfish (named BD-4) from the Southern Ocean (60°29′57" S, 52°11′44"W) on the scientific expedition ship "Xue Long" at the end of 2016. Although the samples were stored and transported by the ship at only −20 °C for more than two month, we successfully extracted the total RNA, and performed molecular species identification and combined analyses of de novo transcriptomics and proteomics. In addition to conventional bioinformatics techniques such as GO and KEGG annotation, we screened and listed toxic proteins, aligned the sequences, simulated three-dimensional structures and performed molecular phylogenetic analysis for typical components, including metalloproteinase and serine proteinase. Our study is the first to identify a polar jellyfish Cyanea sp. with de novo transcriptomics and proteomics, and these data can further serve as a public database for the identification of potential polar jellyfish-derived lead compounds. Species identification. (A) Geographical distribution (left) of the jellyfish captured from Antarctica (60°29′57 "S, 52°11′44" W) and image of the jellyfish that was preliminarily named BD-4 (right). The sampling location is marked in red circles. (B) Phylogenetic tree constructed using mtDNA sequences of cytochrome c oxidase subunit I (MT-COI, CO1) by using MEGA 7 with the Neighbor-Joining method. BD-4 is marked with red circles, lophotrochozoa are marked with dark blue circles, cnidaria are marked with light blue circles and the identity values are indicated on the right of each species name. (C) Two amino acid sequences of CO1 from Cyanea tzetlinii and Cyanea capillata aligned with the CO1 amino acids of BD-4 transformed from the DNA sequence by blastx. At the bottom of the columns, asterisks (*) show conserved positions, and colons (:) show conserved substitutions and points. (D) Phylogenetic tree constructed using the CO1 amino acid sequences of BD-4 and 7 other species using using MEGA 7 with the Neighbor-Joining method. BD-4 is marked with red circles, and the identity values are indicated to the right of each species name. Unlabelled Image • We have luckily captured an Antarctic jellyfish by the Chinese "Xuelong" scientific ship, and naturally did the investigations on it by CO1 molecular identification, combined analysis of transcriptomics and proteomics, as well as its toxin screening. The sample is very precious and this study is the first to identify the polar jellyfish, and its toxin screening. • Our study is the first to identify a polar jellyfish Cyanea sp. with transcriptomics and proteomics, and these data can further serve as a public database for the identification of potential polar jellyfish-derived lead compounds that feasibly function well in the cold environment. [ABSTRACT FROM AUTHOR]