<p>Among eukaryotes, alternative splicing (AS) plays a role in mechanisms involved in processes such as regulation, development, and stress response. In animals, AS mainly functions in tissue development, whereas in plant species, AS plays a major role in stress response, a function additionally mirrored in microalgae. The latter species are highly valued for their ability to produce a variety of useful compounds. Furthermore, their productivity is directly intertwined with stress response, placing the mechanisms behind it in the spotlight. As stress can spur an increased production of pigments, lipids, fatty acids, and carbohydrates utilized in the synthesis of products such as nutraceuticals, pharmaceuticals, and biofuels. Delving into microalgae, we assess AS processes and the regulation of various developmental stages and stress conditions. Additionally, cyanobacteria also have high economic value. As prokaryotes with the ability to undergo self-splicing, research focus has promoted the phylum’s use in biotechnology to catalyze protein splicing. Although self-splicing and AS are two different types of splicing processes, there are some connections between them. For instance, the small nuclear RNA required for AS originates from group II introns. Therefore, this review focuses on elaborating on two distinct but related topics: the AS of microalgae and the three main forms of self-splicing intervening sequences (group I introns, group II introns, and inteins) in cyanobacteria.</p>