Vibrio coralliilyticus is an emerging bacterial pathogen that infects the mucosal surface of corals and has been implicated in bleaching events worldwide. Phage therapy has been suggested as a potential strategy to combat V. coralliilyticus infections across coral reefs. Here we report the complete genome of a lytic bacteriophage, named YC, whose host range is specific to V. coralliilyticus. Phage YC is a member of the T4-like family based on high sequence homology and morphological similarity to bacteriophage T4. Bioinformatic analysis of the YC phage genome revealed that gene gp4, a highly conserved head maturation protein, contains a previously unidentified nuclease domain. The predicted nuclease domain of gp4 shows high sequence homology to transposase A, a protein encoded by transposon Tn7. Transposase A cleaves DNA as part of the cut-and-paste mechanism of Tn7 dispersal. To verify the predicted nuclease capability of gp4, the protein was cloned and expressed in E. coli bacterial host and assayed biochemically. Incubation of purified gp4 with a circular plasmid resulted in degradation of the DNA in vitro. These analyses suggest that gp4 cleaves DNA during viral morphogenesis to enable maturation of the viral particle. Greater understanding of how T4-like phages are assembled will augment phage engineering and improve efficacy of phage therapy treatments.