Oleaginous microalgae have commercial potential as photoautotrophic cell factories capable of producing advanced biofuels and high-value speciality oils. One genus of particular interest is Nannochloropsis, which includes a number of robust marine species well suited to industrial-scale cultivation. Advances in bioprocess technology, together with strain enhancement through traditional mutagenesis or genetic engineering approaches, now offer the possibility of improving the economics of oil production from Nannochloropsis. In this review we describe the current and potential industrial applications of this genus, consider the present status of genetic enhancement methods, and highlight the need for new advances in this area -including the development of techniques for engineering the chloroplast genome.