Diatoms are single-celled microalgae with silica shells or frustules that can form colonies. More than 100,000 species of diatoms have been discovered to date, with cell sizes ranging from 2 to 200 μm with geometries including circular, triangular, square, or elliptical. They contain both organic and inorganic components and these fractions are evaluated for energy application. The organic fraction is utilized to make biofuels for less polluting transportation. The diatom extracted bio-oil contains both saturated and unsaturated fatty acids, which holds potential to improve biofuel quality and quantity. One of the outstanding complexities of the diatom is the multilayered frustule structure. The frustule consists of amorphous hydrated mesoporous silica with an organized microstructure that is much beyond the reach of synthetic design and fabrication technologies. Research on functional materials used in sophisticated energy storage devices, such as batteries and supercapacitors, can benefit from diatoms’ delicate and repeatable nanoscale siliceous structure. This chapter presents the state-of-the-art on diatoms for their utility as biofuel and advanced energy storage systems.