Microsatellite markers were used to investigate the mating system of the Estuarine Crocodile (Crocodylus porosus). Three-hundred and eighty-six hatchlings from 13 clutches from a wild Northern Territory population, and 364 hatchlings from 21 clutches from a captive North Queensland population, were sampled. All samples were genotyped across five microsatellite loci. Multiple paternity was found in 69% of clutches in the wild population compared to 38% of clutches in the captive population. Up to three possible fathers were indicated in some clutches. Shared paternity was suggested by the presence of a common paternal genotype within two clutches in the wild population and among up to three clutches from a large shared pen in the captive population. The probability of detecting multiple paternity at all loci was high; 95% in the wild population and 98% in the captive population. There was no evidence of increased hatching success in the clutches that indicated multiple paternity compared to single paternity clutches in either population (P = 0.43 to P = 0.67). It is unknown whether the occurrence of multiple paternity in C. porosus is a result of multiple mating within the same breeding season or of sperm stored from matings in a previous season. These results suggest the genetic mating system for C. porosus is not polygynous but more likely promiscuous, and there is no evidence of dominant alpha males who control paternity in large areas.