Bacteriophages (phages) are viruses that infect bacteria. Phages are the most abundant and most diverse biological entities on earth. Phages have served as model systems for studying the rules of molecular biology in previous years. However, a lot of phage research was paused due to lack of proper technologies available. Recently, with emerging techniques, e.g. fluorescence microscopy, X-ray crystallography, cryo-EM, and bioinformatics, more and more details of the workings of phages have been unveiled. These new methods will continue to help reveal unprecedented details of phage systems, which will advance our understandings of different processes in these “simple” systems, shed important light on dynamical processes in higher organisms, and promise to transform into new technologies, e.g. combatting drug-resistant bacterial pathogens, for genome editing, etc. This methods collection aims to bring together current methods used to study phages in various aspects, including but not limited to phage decision making, infection dynamics, phage assembly, host-phage interaction, and in general, the infection cycle.