In the past few years, we have contributed efforts to ~1/5 of the reported fish genomes. Based on our related experience, here we outline recent advances in bioinformatics for fish genomics, with an emphasis on development of software for genome assembly, genome annotation and evolutionary analysis. This review will be helpful for the new players of genome analysis on both animals and plants. In the past decade, whole genome sequences of approximately 50 fish species have been reported . We have been involved in ~1/5 of these international works from 2014 to 2017, such as mudskippers (2014) , Chinese large yellow croaker , Chinese barbel fishes , Asian arowana [5,6], Channel catfish , seahorses , Japanese flounder , Chinese clearhead icefish  and Northern snakehead . We are also in charge of the China Auqatic 10-100-1,000 Genomics Program , in which ~100 fish genomes are sequencing targets for the next 3~5 years. Based on our previous experience on fish genomic studies, here we outline recent advances in related bioinformatics for fish genomics to share with public readers. Since the basic informatics includes genome assembly, genome annotation and evolutionary analysis, we discuss them one by one in this order.