However, algal strains and production processes for various pigments or PUFAs require significant improvements to compete successfully with currently used products. Strain improvements by genetic engineering for higher product yields, and promoting the acceptability of transgenic algae in the market and with regulatory authorities are key challenges in promoting the future success of microalgal biotechnology in the high value and bulk product markets. In the specific case of H. pluvialis, the specific challenge is reducing astaxanthin production costs by a factor of 3–4, for accessing the far larger aquaculture feed market with natural pigment. This could be achieved by increasing astaxanthin accumulation, enhancing biomass productivity by means of genetic engineering and simultaneously reducing cultivation costs by moving to cheaper open pond production. Thus, adequate methods for genetic engineering of this commercially important species are required.