The impact of microalgae (including blue-green algae or cyanobacteria) on human life can be both beneficiary and deleterious. While microalgae can be cultivated and used as feedstocks for the production of bioenergy and high value-added products in nutraceuticals, pharmaceuticals, and aquaculture feeds, some microalgae cause harmful algal blooms (HABs) that cause large-scale mortality in aquatic environments around the world. Thus, with the development of microalgal biotechnology and increasing concern about HABs, research on microscopic algae has increased significantly. However, this growth of academic research and application fields has been hindered by difficulties in obtaining axenic cultures. Therefore, this review provides a brief explanation of diverse establishment techniques, along with their strengths and weaknesses, with the hope of facilitating successful axenic cultures. A compilation of research fields and relevant important findings is also presented to clarify the importance of pure algal cultures. Finally, several controversial and sometimes overlooked issues related to the establishment, maintenance, and utilization of axenic cultures are discussed.