To separate polymer fine particles while maintaining the shape by bringing a microorganism having polymer fine particles into contact with a specific functional water capable of solubilizing a cell component other than the polymer fine particles to recover the polymer fine particles and drying the polymer fine particles at a specific temperature.

In a method for separating polymer fine particles synthesized in microbial cells, a microorganism (e.g. Burkholderia cepacia) having the polymer fine particles retained in the cell is obtained and the bacterium is brought into contact with a functional water solubilizing cell component other than the polymer fine particles to afford a mixture containing the polymer fine particles and then, the polymer fine particles are recovered from the mixture and the recovered polymer fine particles are dried at a temperature not higher than the melting point to separate the polymer fine particles. Furthermore, the functional water has pH 1-7, 300-1,500 mV oxidation-reduction electric potential (acting electrode: platinum electrode; reference electrode: silver-silver chloride electrode) and 500-5,000 mg/l effective chlorine concentration.