In South Australia, fishery independent surveys in the blue crab fishery have been conducted on an annual basis in Gulf St Vincent (GSV) and Spencer Gulf (SG) since 2002. The primary aims of the survey are to collect data on the abundance and size composition of blue swimmer crabs (Portunus pelagicus) to assist ongoing assessment of the blue crab stocks. Information has also been collected on incidental captures to support mitigation strategies for reducing by-catch. This survey investigates the relative catch composition from both commercial pots (90mm mesh) and research pots (55mm mesh). A total of 52 by-catch species (29 fish, 9 crustaceans, 10 molluscs, 3 echinoderms and 1 tunicate) were collected during the surveys, none of which are listed under the Environment Protection and Biodiversity Conservation Act 1999 as rare, threatened or endangered. Multivariate analysis confirms that research pots capture higher numbers of by-catch species and individuals than commercial pots. These analyses also reveal large differences in by-catch composition between the two gulfs. An industry sampling program is being implemented to address seasonal variability on by-catch composition and abundance.