Researches on CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) systems, that are adaptive immunity systems encoded by prokaryotes, have promoted the development of new genome-editing tools. Bacteriophages are not only the driving elements for the evolution of prokaryotes' CRISPR arrays, but also the targets of the CRISPR/Cas systems. Studies on functional genomics of bacteriophages have been lagging behind the discovery of new phage strains and the sequencing of their genomes. CRISPR/Cas systems-driven genome engineering of bacteriophages provides a novel approach for bacteriophage functional genomics. This review comments on a few profound cases of genome engineering of bacteriophages that employed the CRISPR/Cas systems, and compares multiple procedures illustrating common or distinct features as well as advantages and disadvantages underlying each procedure. We design new applications of the CRISPR/Cas systems coupled with bacteriophage recombination systems, discuss their potential constraints, and offer suggestions for each option.