Lysogenic conversion genes are derived from integrated phage genomes and the expression of these genes contributes to bacterial host fitness. These genes are not well investigated in marine bacteria nor at the level of the bacterial community. The anoxic layer of the Anoxic Marine Zone (AMZ) off the coast of northern Chile presents a habitat barrier for macrofauna and is the habitat of a thriving microbial community. The AMZ viral community is thought to be dominated by integrated, temperate bacteriophages. Prophage infection appears to be prevalent in the anoxic region of the AMZ; therefore, the lysogenic conversion gene functions were hypothesized to enhance the ability of the AMZ bacteria to persist in the anoxic habitat. Metagenomic samples from the AMZ were compared with samples from a productive, oxic surface environment in Meta Verde (MV), Brazil in which the viral community was expected to be dominated by lytic phages. Total community DNA from the bacterial, free-floating phage and Mitomycin C-induced phage fractions were extracted and pyrosequenced. Eight metagenomes with a total of 1.1 billion bp contained in 3.1 million sequences were obtained. Taxonomic and functional differences between the free-floating and integrated phage communities were found in the three locations, suggesting distinct lytic and temperate phage communities. AMZ prophage genotypes were obtained by cross-assembly of the bacterial, free-floating and integrated phage metagenomes. Functions of the potential lysogenic conversion genes in the AMZ location included those related to chemotaxis. The genetic information of the prophage community provides a natural lens to focus on the genes that are relevant to the bacterial community.