Reliable population estimates are fundamental to the conservation of endangered species. We evaluate here the use of photo-identification (photo-ID) and mark-recapture techniques for estimating the population size of the endangered Saimaa ringed seal (Phoca hispida saimensis). Photo-ID data based on the unique pelage patterns of individuals were collected by means of camera traps and boat-based surveys during the molting season in two of the species' main breeding areas, over a period of five years in the Pihlajavesi basin and eight years in the Haukivesi basin. An open model approach provided minimum population estimates for these two basins. The results indicated high survival rates and site fidelity among the adult seals. More accurate estimates can be obtained in the future by increasing the surveying effort both spatially and temporally. The method presented here proved effective for evaluating population size objectively, whereas the results of the current snow lair censuses are dependent on varying winter conditions, for instance. We therefore suggest that a photo-ID-based non-invasive mark-recapture method should be used for estimating Saimaa ringed seal abundances in order to ensure reliable, transparent population monitoring under changing climatic conditions.