Wedge-tailed Shearwaters and Black Noddies are the two numerically dominant seabird species found in the southern section of the Great Barrier Reef, Australia. This research provides baseline breeding population estimates for nine of 16 islands in the Capricornia Group over five years for Shearwaters (1996–2000) and four years for Noddies (1997–2000). With estimates of ~302 000 active breeding pairs of Black Noddies and ~560 000 breeding pairs of Wedge-tailed Shearwaters in the area, the research results have confirmed the importance of the Capricornia Group as a recognised breeding area for these birds.