Microbial sequence typing has become essential in molecular epidemiology and infectious disease genomics. This book chapter outlines standard and new approaches for microbial sequence typing at gene and genome levels using next-generation sequencing (NGS) technologies. We describe multilocus sequence typing (MLST), multilocus variable-number tandem-repeat analysis (MLVA), ribosomal multilocus sequence typing (rMLST), core genome MLST (cgMLST), whole-genome sequencing (WGS), and next-generation MLST (NGMLST) approaches. To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are required. We discuss several applications of these approaches to disciplines including genotyping, phylogenetics, and molecular epidemiology, presenting guidelines for subsequent analysis, including methods and computational frameworks.