Mercury (Hg) is a contaminant that is impacting ecosystems worldwide. Its toxicity is threatening wildlife and human populations, leading to the necessity of identifying the most affected ecosystems. Therefore, it is essential to identify pertinent bioindicator organisms to monitor Hg contamination. In this study, we determined the stable carbon and nitrogen isotope ratios in the red blood cells (RBCs), and the total Hg concentration in total blood of 72 Melanosuchus niger in French Guiana. The goals of our study were to assess the level of Hg contamination in total blood of Black caimans and to further investigate the influence of individual traits (i.e., sex, size/age, diet) on Hg concentrations. Mercury concentration in total blood of Black caimans ranged from 0.572 to 3.408 μg g−1 dw (mean ± SD is 1.284 ± 0.672 μg g−1 dw) and was positively correlated to individual body size and trophic position . We did not find any sexual or seasonal effects on Hg concentrations in the blood. The use of blood of M. niger is relevant to determine Hg concentrations within the population and suggests that this species can be used as a bioindicator for environmental contamination. In addition, our results emphasize trophic position as a major source of Hg variation and further suggest that it is essential to take trophic position into account for future studies.