Chromium (VI) is a well-known pollutant that is present in industrially polluted soil and water, and has been reported to be mutagenic and carcinogenic. In the present study, we investigated the effective use of Leptolyngbya boryana (cyanobacterium) as an eco-friendly option to overcome Cr (VI) toxicity in tannery effluents. The main objective of this study was to identify the Cr reductase (ChrR) gene and its variability in the context of Cr (VI) stress. Industrial polluted soil samples were collected and processed according to standard protocols for ChrR variation and 16S rDNA gene analysis. Genomic DNA was isolated from the collected samples and the ChrR and 16S rDNA genes were amplified by PCR. Amplified 16S rDNA was sequenced and aligned with known sequences. In the present study, a strong correlation was established between the nucleotide sequences of the ChrR and 16S rDNA genes. The Minimum Inhibitory Concentration (MIC) was determined for Cr (VI), and pure strains of L. boryana were identified and isolated from soil samples. Cr (VI)-stressed conditions and their genetic variability were confirmed by sequencing. In conclusion, the L. boryana strain has been identified an eco-friendly option for overcoming Cr (VI) toxicity in tannery effluents.