Diel periodicity in gene expression patterns of specific microbial groups has been demonstrated for both autotrophic and heterotrophic microbes in coastal and open ocean environments. To better define the spatiotemporal distribution and drivers of these daily oscillations, we investigated how diel periodicity in gene transcription patterns changed with depth from surface waters to the base of the euphotic zone. Diel patterns in microbial community transcript abundances within and below the euphotic zone in the North Pacific Subtropical Gyre were determined from the ocean's surface to 250 m. We examined how the gene and taxon representation as well as magnitude and shape of transcript diel oscillations changed with depth, and how they related to other environmental parameters. Two different diel time series depth profiles were conducted during the course of two Hawaii Ocean Experiment – Budget of Energy (HOE-BOE) expeditions in 2014: HOE BOE cruise 1 (March 13-16, 2014), and HOE BOE cruise 2C (June 16-27, 2014). http://hahana.soest.hawaii.edu/hoeboe/hoeboe.html.