The total number of inhabitants on the Earth is estimated to cross a record number of 9 × 10
3
million by 2050 that present a unique challenge to provide energy and clean environment to every individual. The growth in population results in a change of land use, and greenhouse gas emission due to increased industrialization and transportation. Energy consumption affects the quality of the environment by adding carbon dioxide and other pollutants to the atmosphere. This leads to oceanic acidification and other environmental fluctuations due to global climate change. Concurrently, speedy utilization of known conventional fuel reservoirs causes a challenge to a sustainable supply of energy. Therefore, an alternate energy resource is required that can maintain the sustainability of energy and environment. Among different alternatives, energy production from high carbon dioxide capturing photosynthetic aquatic microbes is an emerging technology to clean environment and produce carbon-neutral energy from their hydrocarbon-rich biomass. However, economical challenges due to low biomass production still prevent the commercialization of bioenergy. In this work, we review the impact of fossil fuels burning, which is predominantly used to fulfill global energy demand, on the quality of the environment. We also assess the status of biofuel production and utilization and discuss its potential to clean the environment. The complications associated with biofuel manufacturing using photosynthetic microorganisms are discussed and directed evolution for targeted phenotypes and targeted delivery of nutrients are proposed as potential strategies to increase the biomass production.