Biofuel production represents an important alternative for replacing fossil fuels and reducing the emission of greenhouse gases into the atmosphere. With increasing demands for renewable fuel to replace fossil fuels, research on new energy sources is becoming more popular and new approaches in research techniques are occurring. In this context, the uses of somatic and gametic embryogenesis, cell suspension, and protoplast fusion in biofuels production will be presented in this chapter. Gametic embryogenesis is a convenient alternative in plant breeding because it makes possible the development of homozygous lines, increasing efficiency and speed in conventional breeding programs. Somatic embryogenesis is an important tool for plant cloning, looking toward the obtaining of improved plants by cell suspension culture or protoplast fusion. Suspension of plant cell cultures has several uses and applications for improving agronomical traits, and it is widely used in biotechnology for micropropagation, for the production of secondary metabolites or other substances, for obtaining somatic hybrids through protoplast fusion, and for modifying plants through genetic transformation. Protoplast fusion has been used by plant breeders to overcome the genetic barriers of outcrossing in incompatible plants, producing hybrid plants with different degrees of ploidy for improved agronomic and horticultural traits. In this chapter, current research with species that have potential to improve biofuel production is presented, with the aim of giving insights on the ways that these techniques can be used to produce renewable fuels.