Mercury (Hg) concentrations in the Amazon are generally high, but no studies have been published on Hg concentrations in caimans (Alligatoridae) from the region. Aiming for sizes representative of caimans traded for food in the Amazon, we measured Hg concentration in tail muscle of spectacled caiman (Caiman crocodilus crocodilus) and black caiman (Melanosuchus niger) from the Purus River basin. The information on Hg concentration in caimans from this area is important because of the potential health risk to humans and other animals that eat them as well as the potential use of these top-level predators as bioindicators. There were no significant interspecific or sex differences in Hg concentrations. The mean Hg concentration was 291.2 μg/kg in C. c. crocodilus and 193.9 μg/kg in M. niger. A significant positive correlation between Hg concentration and size was found for M. niger (p = 0.005) but not for C. c. crocodilus. Our Hg sample from M. niger corresponded to the size of M. niger collected for commercial trade, but our Hg sample from C. c. crocodilus turned out to be significantly smaller than the trade samples (p = 0.004), but this difference is not pertinent in the absence of a correlation between size and Hg concentration for this species. Although there are no standards for reptile meat, both species had mean Hg concentrations lower than the maximum allowable level of 500 μg/kg Hg recommended by the World Health Organization and by the Brazilian Health Ministry for fish. However, by calculating daily consumptions limits and number of meals per month that can be safely consumed, we found that consumers who eat caimans frequently may be at risk for Hg-related health problems.