Before animals reared in captivity can be used as a model for study or as a supplement for wild populations, it is important to demonstrate that they can integrate with high success and without adversely affecting the natural population. For the blue crab Callinectes sapidus (Rathbun, 1896), coded wire tags have been used to positively discriminate hatchery-raised individuals from wild. This technique can be prohibitively expensive, however, due to high start-up costs and manpower needs during implantation, and mortality as a result of the tagging process is also a consideration. To reduce costs and increase the number of possible individuals monitored per unit effort, the suitability of the mitochondrial gene nad2 as a genetic tag to identify hatchery-produced crabs was tested. Batches of juvenile crabs approximately 20 mm in carapace width were implanted with wire tags and released into a variety of locations in the upper Chesapeake Bay. Juveniles were later recaptured from release sites and scanned for wire tags in the field. Tissue samples from recaptured crabs were also sequenced with nad2 specific primers. Comparison of sequences from recaptured individuals to batch mothers showed 95% congruence in positive identification through wire tagging and nad2 sequencing and an ability to discriminate hatchery batches from wild crabs with 97.8% success. Thus, use of an nad2 marker as a genetic tag is as successful as wire tags in C. sapidus with lower costs and mortality.