Bacteriophage PhiJL001 infects a novel marine bacterium in the alpha subclass of the Proteobacteria isolated from the marine sponge Ircinia strobilina. PhiJL001 is a siphovirus and forms turbid plaques on its host. The genome sequence of PhiJL001 was determined in order to better understand the interaction between the marine phage and its sponge-associated host bacterium. The complete genome sequence of PhiJL001 comprised 63,469 bp with an overall G+C content of 62%. The genome has 91 predicted open reading frames (ORFs), and 17 ORFs have been assigned putative functions. PhiJL001 appears to be a temperate phage, and the integrase gene was identified in the genome. DNA hybridization analysis showed that the PhiJL001 genome does not integrate into the host chromosome under the conditions tested. DNA hybridization experiments therefore suggested that PhiJL001 has some pseudolysogenic characteristics. The genome of PhiJL001 contains many putative genes involved in phage DNA replication (e.g., helicase, DNA polymerase, and thymidylate synthase genes) and also contains a putative integrase gene associated with the lysogenic cycle. Phylogeny based on DNA polymerase gene sequences indicates that PhiJL001 is related to a group of siphoviruses that infect mycobacteria. Designation of PhiJL001 as a siphovirus is consistent with the morphology of the phage visualized by transmission electron microscopy. The unique marine phage-host system described here provides a model system for studying the role of phages in sponge microbial communities.