Photoautotrophic microalgae offer a great potential as novel hosts for efficient recombinant protein production.Nannochloropsis oceanicaproduces an extraordinarily high content of polyunsaturated fatty acids,and its robust growth characteristics, published genome sequence and efficient nuclear transformation makeN. oceanicaa promising candidate for biotechnological applications. To establish a robust and flexible system for recombinant protein production, we cloned six endogenous, potentially constitutive or inducible promoters fromN. oceanicastrain CCMP1779 and investigated their strength using monomericVenusas reporter gene. Microscopic pre-screening of individual transformants revealed that the promoters of elongation factor (EF), tubulin (TUB) and nitrate reductase (NR) enabled high reporter gene expression. Comparative quantitative analyses of transformant populations by flow cytometry and qRT-PCR demonstrated the highestVenusexpression from the EF promoter and the NR promoter if extended by an N-terminal 14-amino acid leader sequence. The kinetics of reporter gene expression were analysed during photobioreactor cultivation, achieving Venus yields of 0.3% (for EF) and 4.9% (for NR::LS) of total soluble protein. Since inducible expression systems enable the production of toxic proteins, we developed an auto-induction medium for the NR promoter transformants. By switching the N source from ammonium to nitrate in the presence of low ammonium concentrations, the starting point of Venus induction could be fine-tuned and shifted towards exponential growth phase while maintaining high recombinant protein yields. Taken together, we demonstrate that a model recombinant protein can be produced robustly and at very high levels inN. oceanicanot only under constitutive but also under auto-inducible cultivation conditions.