The present study assessed the presence and prevalence of multiple paternity (MP) in litters of grey reef (Carcharhinus amblyrhynchos) and scalloped hammerhead (Sphyrna lewini) sharks caught in Papua New Guinea. Litter size between species significantly differed with an average of 3.3 pups for grey reef sharks and 17.2 pups for scalloped hammerhead. Using 15 microsatellite loci, we identified multiple paternity in 66% of grey reek sharks (4 out of 6 litters) and 100% multiple paternity in scalloped hammerhead sharks (5 litters) using 10 microsatellite loci. We reported high paternal skew and a positive correlation between adult size and litter size in scalloped hammerheads, but not in grey reef sharks. Differences in the frequency of MP between species and the identification of paternal skew is thought to be affiliated with mating strategies and post-copulatory mechanisms. The presence of MP is thought to benefit populations by enhancing the variation of genetic diversity therefore increasing the population’s genetic resilience to pressures including heavy fishing. Given both species are commonly impacted in local PNG fisheries, results from this study provide useful information for local management in the region.