The field of fish phylogenetics, which examines the evolutionary links between different fish species, has seen a significant upheaval as a result of developments in molecular biology and genomics. The research determine that advancement related to the fish phylogenetics the research based on the theory also numerical analysis. This research offers a thorough summary of this journey from its early stages, which were marked by the usage of few molecular markers, to the present day of next-generation sequencing (NGS) technology. Fish evolutionary links were first deciphered using mitochondrial DNA (mtDNA) and nuclear DNA markers. The molecular markers link with the next generation sequencing related to the advancement between them. These markers could not resolve complex phylogenetic connections, although being informative. Utilising genome-wide data, phylogenomics has become a potent approach for gaining high-resolution insights about the evolution of fish at various taxonomic levels. As more affordable alternatives to whole-genome sequencing, targeted sequencing techniques like ultra-conserved elements (UCEs), RAD-seq, and ddRAD-seq have improved our capacity to study fish phylogenetics. Phylogenetic analysis was eased by the creation of sophisticated bioinformatic software and tools, making it easier for researchers to use. The biogeographic history of fish lineages has been revealed by integrating DNA data with geological and paleontological knowledge, going beyond pure phylogenetics and giving essential context for the evolution of fish. Our understanding of fish diversity has been enhanced by an integrated approach that combines genetic data with morphology, ecology, and behavior. This method has also resulted in the identification and description of new species.