Marine Stramenopiles (MAST) were first described two decades ago through ribosomal RNA gene (rRNA gene) surveys of marine environments. Since then, MAST clades have been found to be abundant and widespread in the ocean, but their biology has remained largely unknown due to the lack of cultivated representatives. Here we use metatranscriptomics to characterize the metabolic activity of MAST cells in the ocean and compare it with that of other heterotrophic flagellates.