Seabird numbers can change rapidly as a result of environmental processes, both naturaland anthropogenic. Informed management and conservation of seabirds requires accurateand precise monitoring of population size. However, for burrow-nesting species this israrely achieved due to spatial and temporal heterogeneity in burrow occupancy. Here,we describe a novel method for deriving more accurate population size estimates thatemploys mark-recapture methods to correct for unknown variation in nest occupancythroughout a breeding season. We apply it to estimate breeding numbers of a colonial,burrowing seabird, the Little Penguin Eudyptula minor, on the Summerland Peninsula,Phillip Island, Australia. Estimates of active burrow numbers during the September 2008to February 2009 breeding season were adjusted to numbers of breeding birds based onburrow occupation and modelled population demographics at six, fortnightly monitoredreference sites. The population was estimated to be 26 100 (95% CI: 21 100–31 100)and 28 400 (23 800–33 000) breeding Penguins in two temporally separated surveyswithin one breeding season. We demonstrate using simulation that the method is robustto variation in burrow occupancy throughout the breeding season, providing consistentand more accurate estimates of population size. The advantage of using the correctedmethod is that confidence intervals will include the true population size. Confidence lim-its widened as burrow occupancy declined, reflecting the increased uncertainty as largeradjustments for low burrow occupancy were required. In contrast, the uncorrectedmethod that uses burrow occupancy alone as a measure of breeding numbers wasinconsistent and significantly underestimated population size across much of the breedingseason. Although requiring considerably more survey effort, the corrected approachprovides a more accurate means for monitoring population changes in colonially breedinganimals while collecting demographic data that can help diagnose the drivers ofpopulation change.Keywords: Australia, Eudyptula minor, Little Penguin, mark-recapture, nest-site occupancy.Population size is a key statistic to monitor howecological processes influence wild populations butaccurate estimates of population size are difficult toachieve for many animals. Many animals, includingseabirds, build nests, which provide a temporallyand spatially stable index of their abundance(Rayner et al. 2007). The most common techniqueto estimate the number of breeding seabirds in largepopulations has been to predict an appropriate timeto survey active nests, assume that each active nestrepresents a breeding pair, estimate density from arepresentative sample of the population, and applythat density to measured areas of occupancy(Lawton et al. 2006, Priddel et al. 2006, Rayneret al. 2007, Reyes-Arriagada et al. 2007, Barbraudet al. 2009, Bragg et al. 2009, Charleton et al.2009, McKechnie et al. 2009, Newman et al. 2009,Scott et al. 2009). While allowing a general popula-tion size to be interpreted, this technique makesnumerous assumptions that are in many casesuntested and may have a large and variable influ-ence on estimates between years. Hence, only largechanges in population size can be detected reliably.