MicroRNAs (miRNAs) are key players in regulation of gene expression at post-transcription level in eukaryotic cells. MiRNAs have been intensively studied in plants, animals and viruses. The investigations of bacterial miRNAs have gained less attention, except for the recent studies on miRNAs derived from Streptococcus mutans ATCC 25175 and Escherichia coli DH10B. In this study, high-throughput sequencing approach was employed to investigate the miRNA population in bacteria of the genus Thalassospira using both the miRDeep2 and CID-miRNA methods. A total of 984 putative miRNAs were identified in 9 species of the genus Thalassospira using both miRDeep and CID-miRNA analyses. Fifty seven conserved putative miRNAs were found in different species of the genus Thalassospira, and up to 6 miRNAs were found to be present at different locations in the T. alkalitolerans JCM 18968 T , T. lucentensis QMT2 T and T. xianhensis P-4 T . None of the putative miRNAs was found to share sequence to the reported miRNAs in E. coli DH10B and S. mutans ATCC 25175. The findings provide a comprehensive list of computationally identified miRNAs in 9 bacterial species of the genus Thalassospira and addressed the existing knowledge gap on the presence of miRNAs in the Thalassospira genomes.