Transcriptome and meta-transcriptome data from two foraminiferal species, Nonionella stella and Bolivina argentea (Foraminifera, Rhizaria). These are two of the most abundant micro-eukaryotic species that inhabit the seafloor of Santa Barbra Basin (California, USA). The primary objective of this project is to identify the different energy metabolic pathways that enabled these benthic foraminifera to survive in oxygen-depleted, sometimes sulfidic sediment.