Rapid loss of marine and terrestrial biodiversity is a result of the global biodiversity crisis. Managing species diversity becomes crucial. DNA barcoding is a new technique for identifying biological items and managing species diversity. In our research, we used the freshwater pipefish Microphis brachyurus. We analyzed intra-species variations discovered in the barcode regions of samples from Tamilnadu, India, and Chiba, Japan. Multiple sequence alignment with CLUSTAL 2.0.10 was used to analyse intra-species variations. SNPs have been found in freshwater pipefish collected from Indian seas, according to the results.