Infectious diseases pose a significant burden on human, animal, and plant populations worldwide. Various organisms, including viruses, bacteria, fungi, and worms, are responsible for these diseases. New pathogens are emerging constantly, while older ones adapt to their environment, evolving and changing. The genetic variation mechanisms of pathogens significantly influence how they interact with their hosts, the diseases they cause, and how they evolve and spread across time and space. Recent advancements in pathogen molecular diagnostics, genotyping, and sequencing, combined with the collection and analysis of complex epidemiological data, have become invaluable tools for understanding the transmission of infectious diseases. This knowledge is crucial for predicting, preventing, and controlling the spread of infections in any population. Molecular epidemiology integrates molecular data from pathogens with epidemiological data collected from hosts to solve public, animal, or plant health issues. For instance, molecular and epidemiological data can be used together to track the spread of a pathogen, identify the source of microbiological contamination, and guide the management of current and future disease outbreaks. This course covers the foundational principles of molecular epidemiology as applied to infectious diseases.