PROBLEM TO BE SOLVED: To find a microorganism capable of removal of a fatty acid in a fatty acid-containing substance, and provide a technique to use the microorganism for removal of the fatty acid in the fatty acid-containing substance.SOLUTION: Microorganisms belonging to Prototheca can exhibit the action to remove a fatty acid from a fatty acid-containing substance even in an environment of a low nutritional state and a high C/N ratio, and can efficiently remove the fatty acid in the fatty acid-containing substance.