In the last decade, antimicrobial resistance has been widespread in several bacterial species. This increase in resistance could be associated with an increase in the use of different antimicrobials to treat infections caused by pathogenic bacteria. While resistance to antimicrobials is often attributed to known mechanisms, other mechanisms are still under investigation for many bacterial species. Detection of antimicrobial resistance often involves conventional agar, broth or disk diffusion assays. However, these methods can be cumbersome and time consuming compared to molecular methods. Consequently, several polymerase chain reaction (PCR) techniques have been developed to expedite the detection of antimicrobial resistance in bacterial pathogens. PCR-based technologies are rapid, sensitive and specific for detecting antimicrobial resistance. Application of such technologies in diagnostic laboratories can provide insight into emerging mechanisms of antimicrobial resistance in veterinary pathogens. In this chapter, we describe molecular mechanisms of drug resistance in microbial pathogens and the potential advantages and disadvantages of PCR-based methods.