This study aims to characterize the microbial community and its relationship with heavy metal pollution in the beaches of Sugozu, an important nesting site for the green turtle. Heavy metal concentrations of sand samples from subregions of Sugozu were determined using ICP-MS. The microbial community was analyzed using the Biolog (R) EcoPlate. The relationship between microbial catalytic activity and heavy metal levels were analyzed using canonical correspondence analysis. Levels of Al-27, Fe-57, Mn-55, and Cr-52 were quite high (4332.34, 13,764.77, 590.98, and 48.21 mg/kg, respectively). The microbial community in subregions with high levels of metals was found to use carboxylic acid as a carbon source. Bioactivity, substrate utilization, diversity, and evenness values indicated negative correlations concentrations of Al-27, Fe-56, and Cr-52 (-0.820, -0.508, and -0.560, respectively). It was also found that microbial diversity decreased in the subregions where heavy metal concentration increased. Embryonic deaths were found highest at early stage (0.1 to 0.2 eggs) and lowest at middle stage for whole study sites by inspecting a total 6408 eggs of 63 green turtle nests. The Biolog EcoPlate was firstly applied to determine pollution, and our findings clearly demonstrate the applicability and effectiveness of this method in assessing nesting beaches.