Chlamydomonas is a recognized, widely used model photosynthetic organism. The survival of Chlamydomonas respiratory-deficient mutants under phototrophic conditions has enabled the dissection of the biogenesis of the mitochondrial respiratory complexes using both biochemical and genetic approaches. This chapter provides an overview of the organization, replication, expression, and translation of the algal mitochondrial genome, a small linear molecule of 15.8kb. Furthermore, the main components of oxidative phosphorylation (OXPHOS), complexes I–V are described and compared with those in other model organisms including as yeast, human and Arabidopsis. In addition, the roles of several OXPHOS-related components, including alternative dehydrogenases and oxidases, as well as uncoupling proteins, are discussed. Finally, the chapter addresses a few other key processes that occur in the algal mitochondrion, such as the production and enzymatic scavenging of reactive oxygen species, the import of nucleus-encoded proteins, and the maturation of iron–sulfur proteins.