The Cantabrian brown bear Ursus arctos population can be seen as a paradigm in conservation biology due to its endangerment status and genetic uniqueness. Therefore, the need to obtain basic demographic data to inform management actions for conservation is imperative. Despite this, empirical data on the size and trends of the Cantabrian bear population are scarce. Here we present the first estimates of population size (N_c) and effective population size (N_e) of the whole Cantabrian brown bear population. We genotyped 270 non-invasive samples collected during 2006 throughout the entire range of the population and subsequently identified 130 individuals. Different model estimators of N_c based on capture—markrecapture (CMR) procedures were compared. The average for the best three models (Mh Chao, Mh Darroch and CAPWIRE TIRM) yielded a total estimate of N_c = 223 individuals (CI_95% = 183–278) and N_e 50 (CI_95% = 36–75) providing an N_e / N_c ratio of 0.22. Estimates for the two subpopulations commonly recognized in the Cantabrian range were N_c = 203 (CI_95% = 168–260) and N_e = 47 (CI_95% = 36–70) for the western subpopulation and N_c = 19 (CI_95% = 12–40) and N_e= 9 (CI_95% = 8–12) for the eastern subpopulation. These data suggest that the Cantabrian brown bear population has increased recently, mainly in the western subpopulation, after a long period of decline and isolation which lead to the split of the population at the beginning of the 20th century. Population sizes in the early 1990s were thought to be only 60 individuals for the western subpopulation and 14 individuals in the eastern one. The efforts to improve conservation policies made since then have probably contributed, to some extent, to the population increase during the last couple of decades.