The ratios of stable isotopes 18 O/ 16 O and 13 C/ 12 C, in sagittal otolith carbonate from two tropical demersal teleosts, red emperor Lutjanus sebae and Rankin cod Epinephelis multinotatus , from several locations in northern Western Australia, differed between sites. On a broad scale, fish from the four locations, Shark Bay, Ningaloo, Pilbara, and Broome had stable isotope values that were sufficiently different to indicate separate stocks, and it is appropriate to manage these populations of the two species independently in these areas. On a smaller scale, there may be limited mixing of these species between the Pilbara trawl fishery and the trap and line fisheries operating out of Onslow and Broome. Values of stable oxygen isotopes were strongly related to sea surface temperature, although there were some sites in shallow water where low values of stable oxygen isotopes indicated that fish were living in warm water. The use of stable oxygen and carbon isotope values is a valuable, cost effective method of determining the degree of mixing of fish stocks.