To identify non-coding RNAs in Haloferax mediterranei through high-throughput RNA sequencing, bioinformatics analysis and molecular techniques.After H. mediterranei cells under log phase of growth were treated with different salt concentrations for 30 minutes, total RNA was extracted for the following strand-specific RNA sequencing and differential RNA sequencing. These RNA-seq data were used to identify the genome-wide ncRNAs and to predict the 5' and 3'-ends of the transcripts by bioinformatics analysis. A few selected ncRNAs were further confirmed by Northern blotting and Circularized RNA reverse transcription-PCR analysis.We identified 105 highly credible ncRNAs. Expression of four ncRNAs showed difference in different salt concentrations. We confirmed the expression, length of transcripts, transcription start and termination sites of incRNA1436 and incRNA1903 by Northern blotting and CR-RT-PCR.We identified the ncRNAs of H. mediterranei in a genome-wide scale, including identification of a few ncRNAs involved in the responses of H. mediterranei to different salt concentrations. Our results have provided fundamental data and novel insights for future study of the function of ncRNA in haloarchaea.