Mitochondrial genome is circular double stranded DNA molecule in most of the eukaryotic organism which is ubiquitously present in all cells as it associated with production of energy. The number of complete mitochondrial genomes sequenced has been increasing day by day. Till date, the complete mitochondrial genome more than 2000 fish species can be retrieved from the NCBI GenBank. Like other vertebrates, fish mitochondrial genome contains 37 genes which include 22 tRNAs, 2 rRNAs (12S & 16S), 13 protein coding genes and one noncoding regions (Control region). The length of fish mitochondrial genome varies based on the size of noncoding region (CR). The complete mitochondrial genome sequence length varies from species to species. This comparison of genome sequences envisage the variations are mostly in the control region as it is highly evolved than other genes of mitochondria. Its mutation rate is very high. Therefore more numbers of indels and intergenic sequences are found. It may be due to the genetic drift, relaxed functional constraint and reduced selection pressure in the evolution of fish mitogenomes.