Because bacterioplankton production rates do not vary strongly across vast expanses of the ocean, it is unclear how variability in community structure corresponds with functional variability in the open ocean. We surveyed community transcript functional profiles at eight locations in the open ocean, in both the light and in the dark, using the genomic subsystems approach, to understand variability in gene expression patterns in surface waters. Metatranscriptomes from geographically distinct areas and collected during the day and night shared a large proportion of metabolic functional similarity (74%) at the finest metabolic resolution possible. The variability between metatranscriptomes could be explained by phylogenetic differences between libraries (Mantel test, P < 0.0001). Several key gene expression pathways, including Photosystem I, Photosystem II and ammonium uptake, demonstrated the most variability both geographically and between light and dark. Libraries were dominated by transcripts of the cyanobacterium Prochlorocococcus marinus, where most geographical and diel variability between metatranscriptomes reflected between-station differences in cyanobacterial phototrophic metabolism. Our results demonstrate that active genetic machinery in surface waters of the ocean is dominated by photosynthetic microorganisms and their site-to-site variability, while variability in the remainder of assemblages is dependent on local taxonomic composition.