A decade-long study of viral abundance at the Bermuda Atlantic Time-series Study (BATS) site recently revealed an annually recurring pattern where viral abundance was fairly uniform in the well-mixed upper water column each winter, yet a subsurface peak in viral abundance between 60 and 100 m depth developed each summer during water column stratification (Parsons et al. 2012; ISME J 6:273–284). Building upon these findings, this study tests the hypothesis that in the well-mixed period (March), the viral communities at the surface and at 100 m depth are similar in composition, while during water column stratification (September), differences in the viruses occupying these 2 depths emerge. Amplification and sequencing of 3 signature genes (g23, phoH, and the ssDNA phage major capsid protein) in addition to randomly amplified polymorphic DNA PCR gel banding patterns were used to assess the structure of viral communities. The 4 data sets revealed similar communities at the surface and 100 m in March when the upper water column was mixed, and divergent communities during September stratification. Water density was found to be a significant driver of viral community variability, with surface communities during September water column stratification significantly different from all other communities. These data demonstrate the importance of water column stratification for structuring viral community composition at the BATS site, either directly through altering the physical conditions, such as ultraviolet radiation, that the viral communities are exposed to or indirectly through structuring bacterial host communities.