Abstract:Next generation sequencing (NGS), which is also known as deep, highthroughput or massively parallel sequencing. It can simultaneously determine the sequences of hundreds of thousands to millions of nucleic acid molecules at one time. Applications in livestock and poultry diseases include complex diagnosis and intensive surveillance, etiology, genomics, evolution and epidemiology, as well as hostpathogen interactions and infection biology. This review first briefly introduces deep sequencing technology, and explains the application progress of deep sequencing in the diagnosis of livestock and poultry diseases through examples. This provides some reference for future related research.