Poly(3-hydroxyoctanoate-co-3-hydroxy-10-undecenoate)s (PHOUs) with controlled amounts of unsaturated side chains were produced by Pseudomonas oleovorans from various mixtures of 10-undecenoic acid and octanoic acid. Epoxidation of the unsaturated side chains in PHOU, by reacting the polymer with m-chloroperbenzoic acid (MCPBA) in homogeneous solution, was readily carried out. After complete epoxidation, changes in the molecular weights and thermal transitions of the PHOUs were investigated by gel permeation chromatography (GPC) and differential scanning calorimetry (DSC), respectively, and the thermal stabilities of the initial and epoxidized polymers were measured by thermogravimetric analysis (TGA). The acidic conditions used for the epoxidation reaction did not result in a significant decrease in molecular weight of the PHOUs. The epoxidized PHOUs were completely soluble, indicating that cross-linking did not occur, but transformation of the vinyl groups in PHOU into epoxide groups caused a decrease in the melting temperature and the enthalpy of melting. In contrast, the glass transition temperatures increased in a linear manner with epoxide group content in the product polymer, and the thermal degradation behavior of the epoxidized polymer was considerably different from that of the initial polymer.