The Applied Genomic Epidemiology Handbook: A Practical Guide to Leveraging Pathogen Genomic Data in Public Health provides rationale, theory, and implementation guidance to help public health practitioners incorporate pathogen genomic data analysis into their investigations. During the SARS-CoV-2 pandemic, viral whole genome sequences were generated, analyzed, and shared at an unprecedented scale. This wealth of data posed both tremendous opportunities and challenges; the data could be used to support varied parts of the public health response but could be hard for much of the public health workforce to analyze and interpret, given a historical lack of experience working with pathogen genomic data. This book addresses that gap. Structured into eight wide-ranging chapters, this book describes how the overlapping timescales of pathogen evolution and infection transmission enable exploration of epidemiologic dynamics from pathogen sequence data. Different approaches to sampling and genomic data inclusion are presented for different types of epidemiologic investigations. To support epidemiologists in diving into pathogen genomic data analysis, this book also introduces the analytic tools and approaches that are readily used in public health departments and presents case studies to show step-by-step how genomic data are used and evaluated in disease investigations. Despite the breadth of scientific literature that uses pathogen genomic data to investigate disease dynamics, there remains little practical guidance to help applied epidemiologists build their ability to explore epidemiologic questions with pathogen genomic data. This handbook was written to serve as that guide. Including case studies, common methods, and software tools, this book will be of great interest to public health microbiologists or lab directors, bioinformaticians, epidemiologists, health officers, academics, as well as students working in a public health context.