Reproductive rate is a key demographic parameter of life history and population ecology. In traditional population-ecology studies of small mammals, this and other vital rates are inferred from capture-mark-recapture (CMR) data. However, CMR assumes that immigrants at first capture can be distinguished from unmarked locally born offspring, an assumption not always met. We verified CMR estimates of locally born red squirrel (Sciurus vulgaris) offspring as a measure of reproductive rate, with candidate offspring (CO)–candidate parent (mothers, CPs) assignment by CERVUS, using ten DNA microsatellite loci. Seventytwo of 122 candidate offspring (59%) were assigned to 52 of 125 CPs in six populations. Estimates of mean litter size were 1.5 young (range 1–3). The 50 CO (41%) not assigned to a reproducing female in the study site were considered immigrants. Parentage assignment also provided evidence of dispersal between two of our sites. Overall, CMR and CERVUS agreed in 77% of cases. Considering only the 55 juveniles determined as locally born by CMR, 50 (91%) were also assigned as local offspring with CERVUS. The main discrepancy between the two methods was that 22 subadult squirrels classified immigrants by CMR, were assigned by CERVUS to females which had reproduced in our sites. It is concluded that although in our study system agreement between CMR and CERVUS in determining local offspring was high, using genetic parentage assignment helped to correctly classify some subadults, considered immigrants by CMR, as locally born. Hence, in largescale demographic studies, combining CMR with parentage assignment will allow more precise estimates of reproduction and dispersal.