Female sea turtles are promiscuous, with clutches of eggs often sired by multiple males and rates of multiple paternity varying greatly within and across species. We investigated levels of multiple paternity in loggerhead sea turtles (Caretta caretta) from three rookeries in Western Australia by analysing polymorphic species-specific genetic markers. We predicted that the level of multiple paternity would be related to female population size and hence the large rookery at Dirk Hartog Island would have higher rates of multiple paternity than two smaller mainland rookeries at Gnaraloo Bay and Bungelup Beach. Contrary to our prediction, we found highly variable rates of multiple paternity among the rookeries that we sampled, which was unrelated to female population size (25% at Bungelup Beach, 86% at Gnaraloo Bay, and 36% at Dirk Hartog Island). Approximately 45 different males sired 25 clutches and the average number of sires per clutch ranged from 1.2 to 2.1, depending on the rookery sampled. The variance in rates of multiple paternity among rookeries suggests that operational sex ratios are variable in Western Australia. Periodic monitoring would show whether the observed patterns of multiple paternity for these three rookeries are stable over time, and our data provide a baseline for detecting shifts in operational sex ratios.