The mating system of the spectacled caiman (Caiman crocodilus) was investigated in the Piagaçu-Purus Sustainable Development Reserve, Amazonas, Brazil. We used six polymorphic microsatellite loci to genotype 15 females and 174 hatchlings representing 20 nests sampled over four consecutive reproductive seasons (2007 to 2010). Paternity was determined by two methods: simple counts, and statistical analysis using Gerud 2.0. Results were congruent between the two approaches, and the null hypothesis of single paternity was rejected in 19 of the 20 nests analyzed, thereby demonstrating that C. crocodilus females are polyandrous and that the breeding system of the species can be characterized as polygamous. The data suggest that one to four fathers were responsible for the paternity of the offspring, and that the males contributed differently (9%-100%) to each of the 20 nests. A total of 53 males copulated with the 20 females mothering the nests. This is the first study on the mating system of C. crocodilus and the frequency of multiple paternity is among the highest values (95%) reported thus far for crocodilians.