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The Port Jackson Shark (Heterodontus portusjacksoni) is an epibenthic, oviparous species endemic to the southern half of Australia. Understanding the genetic structure, ecology and reproductive behaviours of this species is essential for developing appropriate management and conservation strategies. However, research has been hampered due a lack of suitable genetic markers. Here, we developed 12 microsatellite loci for H. portusjacksoni. The number of alleles at these polymorphic loci ranged from 3 to 22 and the observed heterozygosity ranged from 0.15 to 0.84. Six of twelve loci successfully cross-amplified in the closely related Crested Hornshark, H. galeatus (Günther, 1870). These markers will aid in studying the spatial and reproductive ecology of H. portusjacksoni and other heterodontid sharks.