Microalgae have been widely recognized as promising hosts for production of various valuable compounds. However, low expression or silencing of transgenes in most microalgae species have hindered their broader implementation in biotechnological applications. In many eukaryotes, intron mediated enhancement (IME) of gene expression by inclusion of introns in heterologous sequences has resulted in a significant increase in transgene expression. This phenomenon has been found in a broad range of eukaryotic organisms including animals, plants, yeasts, and more recently green microalgae. However, no investigation has been conducted in diatoms. Here, we present findings of IME in the oleaginous diatom, Fistulifera solaris. Inclusion of a native intron found in glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene into a bleomycin-resistance gene (shble) resulted in enhancement of the mRNA level of shble, leading to increase in resistance and selection. We tested this IME in a heterologous plant sesquiterpene synthase gene construct (AgBS), leading to expression approxi- mately double that of non-intron containing cassettes. The heterologous AgBS lead to accumulation of the sesquiterpene (E)-α-bisabolene, indicating that native precursors were amenable to manipulation and available in the cytoplasm of this diatom. To the best of our knowledge, this is the first study to investigate the effect of IME in diatoms.