Currently, the diagnosis methods applied in bacteriology and virology are frequently focused at modern molecular methods such as polymerase chain reaction (PCR), real-time PCR, loop-mediated isothermal amplification (LAMP) or confirmatory methods for already identified infectious agents of animals such as high throughput sequencing- HTS, or next-generation sequencing (NGS). A number of these methods are officially recommended by the World Organisation for Animal Health (OIE) for the routine diagnosis of major animal diseases with the greatest economical impact. The aim of this paper is to provide to a reader an overview on recent genomic methods used in diagnosis of infectious animal diseases along with their advantages and limitations. These methods facilitate efficient and reliable identification of animal pathogens and allow to characterize and sometimes to identify a newly recognized species of bacteria and viruses.