Sydney rock oysters Saccostrea glomerata are among the most important estuarine species on the eastern coast of Australia and also the basis of a major aquaculture industry. The industry now largely relies on Sydney rock oysters that have been selectively bred for fast growth and disease resistance. Selectively bred S. glomerata are currently farmed in estuaries that also sustain wild populations of Sydney rock oysters, providing the opportunity for interbreeding. This has led to concern that gene flow from farmed, selectively bred oysters could alter the genetic variability of wild oyster populations. Here, we use next-generation genotype-by-sequencing to test for genetic introgression between wild and farmed, selectively bred (B2 line) Sydney rock oysters from 2 sites in the Georges River, NSW. Strong genetic partitioning was identified between the wild and selectively bred populations. There was no evidence of gene flow in the form of introgression, even though selectively bred B2 oysters have been farmed in the Georges River since the early 1990s. Contrary to our expectations, we also found significantly higher levels of genetic diversity and heterozygosity in the selectively bred population relative to the wild population. The relatively low level of genetic diversity that we detected in wild oysters may be particularly relevant to the adaptive capacity of this species in the wild.