Isoamylase (EC 3.2.1.68), belonging to glycoside hydrolase subfamily GH13_11, catalyzes the hydrolysis of the 𝜶-1,6-D-glucosidic linkages in amylopectin, glycogen, and derived oligosaccharides. The high debranching efficiency and transglycosylation activity enable its use in food, feed, detergent, and other industries. However, the low catalytic efficiency and insufficient stability of currently known isoamylases prevent their widespread applications. To meet the requirements set by specific applications, therefore, there is a continuing demand to obtain isoamylases with good stabilities and high expression levels by protein engineering and development of novel fermentation strategies. Herein, the microbial sources, biochemical properties, and distinct sequence and structural features of microbial isoamylases are summarized. Current developments in the protein engineering, heterologous expression, and industrial applications of isoamylases are also discussed. Finally, the future research perspectives of microbial isoamylases are provided.