Polyhydroxyalkanoate (PHA) copolymers consisting of 3-hydroxybutyrate, 2-hydroxy-4-methylthiobutyrate (2H4MTB), and 2-hydroxy-4-methylvalerate were biosynthesized from recombinant Escherichia coli using L-methionine as the 2H4MTB precursor. The 2H4MTB unit contains a sulfide group in its side chain that can be oxidized to sulfoxide and sulfone groups by oxidants, thereby increasing the hydrophilicity of the polymer. The PHAs were biosynthesized at 3.9, 9.2, and 13.9 mol% 2H4MTB, and their polymer films were oxidized with hydrogen peroxide. The surface of the oxidized film was characterized using Fourier-transform infrared spectroscopy, Raman spectroscopy, and contact angle analysis. The oxidized films with 13.9 mol% 2H4MTB showed a 30° lower water contact angle than the non-oxidized films. To assess their biodegradability in seawater, the PHA films were immersed for 114 days in seawater continuously pumped from two depths (24 and 397 m) in Suruga Bay, Shizuoka, Japan. The weight loss of the films immersed in deep seawater was higher than that of those immersed in surface seawater. Additionally, there was a tendency for higher degradation of the oxidized films than that of the non-oxidized films, which was also confirmed by the biochemical oxygen demand test. In the surface morphology analysis by scanning electron microscopy, irregularities were observed in the degraded films, but their morphologies differed between the oxidized and non-oxidized films. Based on these observations, the biodegradation of the PHA films in seawater is discussed.