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The progress in the sequencing technology has significantly augmented single nucleotide polymorphism (SNPs) discovery and genotyping in fish genetic research. The affordable cost, development in Next Generation Sequencing (NGS) technology and computational tool has rationalized SNPs discovery in various model and non-model aquaculture species. The SNPs linked with biological part on a genomic scale is expected to provide new insights into the fish biology, evolution and physiology. Alongside, recently developed SNPs arrays are a powerful tool for understanding genomic patterns of fish diversity, phylogeny in fish populations and marker–trait associations. These SNPs arrays or chips are a valuable for genetic studies in fish species like genomic selection, Quantitative Trait Locus (QTL) detection, and genetic diversity studies. Here, we have discussed for SNPs discovery using advanced sequencing techniques for understanding genomic level information in fishes and provide a future perspective. We have speculated the impact analysis of SNPs on the genes/proteins, which rationalize further experimental study. This review focuses on high-throughput sequencing technologies has used for SNPs identification studies in fishes with evidence. This review will simplify process for mining SNPs from important genes associated with the production/performance traits for conducting genomic selection program in aquaculture.