Fishes are by far the most species-rich group of vertebrates, with 36,105 species currently recognized, approximately the same number of species as that of all non-fish vertebrates combined. Recent decades have witnessed dramatic population declines for many fish species, together with a loss in overall fish biodiversity. Globally, fish biodiversity is being threatened by a multitude of anthropogenic impacts including overfishing, habitat loss, pollution, aquaculture, loss of river connectivity, climate change and the impact of alien species. Nowhere is the world’s biodiversity crisis more acute than in freshwater ecosystems. While rivers, lakes and wetlands cover less than 1% of the planet’s total surface, they are home to over half the world´s fish species. One-third of freshwater fishes are now threatened with extinction, and 80 species have become extinct in recent years. This review covers the main drivers of declining fish biodiversity and details remedial strategies aimed at conserving both marine and freshwater fish biodiversity. The preservation of genetic resources through the cryobanking of reproductive cells and tissues, collectively known as germplasm, will increasingly become a valuable tool in the conservation of fish biodiversity. It is expected that the ability to establish cryobanks for the full range of fish germplasm, including sperm, oocytes, embryos and germ cells will be of key importance to the conservation of threatened fish species, as well as to fishery management and aquaculture. With the help of a range of emerging reproductive technologies, frozen germplasm will play a key role in future in situ and ex situ conservation initiatives. The rapid advance in next-generation sequencing technologies, together with the proliferation of resources such as fully sequenced fish genomes, is expected to result in a rapid expansion in the application of conservation genomics to the field of fish conservation and be instrumental in formulating future management strategies directed at conserving fish biodiversity, through both in situ and ex situ conservation initiatives.