From a conservation standpoint, species that are managed without consideration of their population sizes and connectivity have the potential to be over-exploited and/or incur population decline. The burrowing shrimp, Trypaea australiensis, is an important ecosystem engineer and fishery resource caught in large numbers for which population information is unknown for properly managing the species. Here, we determined the level of population structure of T. australiensis across three locations along the East Coast of New South Wales, Australia, using genome-wide single nucleotide polymorphisms (SNPs) obtained through double digest Restriction-site Associated DNA-sequencing (ddRAD-seq). Analysis of population structure, including pairwise Fst (−0.003 to −0.001), STRUCTURE (K = 2) and Discriminant Analysis of Principal Components (DAPC) showed no evidence of structure among locations. Our findings provide crucial preliminary population genetic data for a key cryptic species, that also suggests gene flow among sampling locations enables the management of fisheries throughout the study area as a single unit.