Livestock metagenomics is the study of genetic materials (nucleotide sequences), directly recovered from livestock’s different organs such as the intestine, mouth, etc. Advancements in multiple sequencing techniques such as 16S rRNA, whole genome sequencing (WGS), etc. have made conducting metagenome analysis possible. Despite the great advancement in computational efficiency, the complexity of the environmental samples from domestic animals often makes purification of DNA challenging. The practical applications of metagenomics are vast-ranging, resulting in the generation of data from soil, water, mines, and the human body to livestock. In this chapter, I will emphasize the use of metagenomic approaches to explore the populations of microbes and their role in livestock health. Isolating DNA from a livestock sample is the first step of any metagenomic study. This is followed by sequencing the extracted DNA through one of the sequencing approaches and multiple sequence alignment with the existing microbial databases such as Greengenes, SILVA, etc. Functional annotations of such a metagenome in the presence of marker genes can also be inferred. Pathogens present in livestock also acquire antimicrobial resistance (AMR) genes. In this chapter, I will focus on the impact of antibiotic resistance genes (ARGs) on global public health. Overall, in this chapter, metagenomics will be explored in terms of the impact of the microbial population in livestock industries. We will also learn how to conduct a step-by-step veterinary metagenomic data analysis by taking pig cecum metagenome data as an example.