The use of micro-algae as a biotechnology platform lags behind other microorganisms especially bacteria and yeast. This is somewhat surprising given the ability to grow algae at very large scale in a cost effective manner. These attributes, and the fact that algae require only sunlight as an energy source and sequester CO2 during the production of biomass, make micro-algae a particularly attractive system for the production of proteins or lipids at very large scale, including the production of biofuels. In order to fully exploit the advantages of micro-algae for biotechnology applications we have been developing tools for the regulated expression of recombinant proteins in the chloroplast of the eukaryotic green algae Chlamydomonas reinhardtii. We have expressed a number of proteins including human antibodies and antibody-toxin fusion proteins, and have shown that these proteins fold and assemble correctly and in the case of the antibody-toxin fusions, bind lymphoma tumor cells and efficiently kill them. More recently we have begun to develop tools for metabolic engineering of algal chloroplast as a means to alter the accumulation of biofuel molecules, and have introduce biosynthetic enzymes to modify isoprenoid biosynthesis in chloroplasts. Eukaryotic algae offer tremendous potential for the large scale and cost effective production of protein therapeutics. Algae also have great potential to be a source of renewable biofuels that can be produced at the scale required to impact global energy needs without adversely impacting food production.