Diatoms play a major role in ocean biogeochemical cycles and are important tools in bioengineering for natural products and nanotechnology. Diatoms and other algae growing at varying resource-limited growth rates allocate carbon to different metabolic pathways to optimize growth; however, the molecular mechanisms controlling these pathway gating strategies are not well understood. We used RNA-Seq to investigate how the model diatom Thalassiosira pseudonana balances photosynthetic energy flux in cells grown in continuous culture under slow and fast light-limited growth rates. We explored fold-change thresholds for differential expression in cells grown under low light (5 µE) with a steady-state growth rate of 0.20 d-1 and cells grown under high light (200 µE) with a steady-state growth rate of 1.54 d-1. Under the conservative threshold (|fold change| > 4, p < 0.05), only approximately 5% of genes were differentially expressed between low and high light conditions. Under the less conservative threshold (|fold change| > 2, p < 0.05), approximately 25% of genes were differentially expressed. Under both thresholds, the majority of differentially expressed genes were not annotated in the KEGG database, highlighting the need for further efforts in functional annotation of diatom genomes. Several genes involved in the TCA and glyoxylate cycles, photorespiratory pathway, and peroxisomal functioning were differentially expressed. Slow-growing cells upregulated genes involved in carbon conservation (i.e., gluconeogenesis and the glyoxylate cycle) and downregulated genes involved in carbon catabolism (i.e., glycolysis). This research identified patterns of gene expression that help explain fundamental differences in metabolic flux in response to growth rate limitation in T. pseudonana. The genes identified in this study are well-conserved across phytoplankton groups, suggesting that they function as master regulators of carbon flux and macromolecular composition in algae. Knowledge of the relationship between growth rate and expression of master regulatory genes may allow for rapid assessment of phytoplankton growth rate in situ, a major goal of oceanographers interested in measuring primary production. This knowledge will also facilitate prediction of cellular responses to a changing climate and increase the feasibility of manipulating metabolic flux for bioengineering and production of important natural products.