Squalene synthase (SS) is an essential enzyme in eukaryotic systems responsible for an important branch point in isoprenoid metabolism that leads to sterol formation. The mechanistic complexity of SS has made it a difficult enzyme to study. The green alga Botryococcus braunii race B possesses several squalene synthase-like (SSL) enzymes that afford a unique opportunity to study the complex mechanism of triterpene biosynthesis. SSL-1 catalyzes presqualene diphosphate (PSPP) formation, which can either be converted to squalene by SSL-2 or botryococcene by SSL-3. A rationally designed mutant study of B. braunii squalene synthase (BbSS) and SSL-3 was conducted to understand structure-function relations among these enzymes. These studies revealed two amino acid positions in SSL-3 (N171, G207) that appeared to control 1’-3 versus 1’-1 linkages. The reciprocal mutations in the corresponding positions of BbSS did not convert this enzyme into a botryococcene synthase. Next, a genetic selection was developed to evolve SSL enzymes towards a fully functional SS. Previous studies have shown that Saccharomyces cerevisiae squalene synthase (ScSS) can be knocked out and although lethal, growth can be restored by providing an exogenous source of ergosterol. Additional studies have shown that successful complementation of the ScSS knockout with a non-fungal SS is possible but requires a fungal SS carboxy- terminus region. Given these observations, proof-of-principle experiments were conducted to demonstrate that SSL-SSL fusion enzymes could complement the ScSS knockout followed by construction of a mutant SSL-SSL fusion enzyme library that was screened in the ScSS knockout yeast line. From this library, mutant SSL-SSL fusion enzymes were identified that were able to complement, which demonstrated the feasibility of this approach as a genetic selection for mutant SSL enzymes. Squalene and botryococcene have valuable industrial applications in vaccine adjuvant formations, cosmetic products, and renewable energy feedstock material. Limitations in natural sources of these molecules have made heterologous production of them an important research target. Algae represent a desirable group of organisms that could be engineered to produce these metabolites because they are photosynthetic and capable of using non-arable farmland. The feasibility, approach, and progress for engineering green algae to produce squalene and botryococcene are discussed.