Ecologists often rely on unique natural markings to identify individual free-ranging animals without disturbing them. We developed a computer-aided photo-identification system for identifying polar bears (Ursus maritimus) based on whisker spot pattern recognition. We automated our system so that the selection of 3 reference points on the input image is the only manual step required during image preprocessing. Our pattern-matching algorithm is unique in that the variability within spot patterns is considered fully rather than representing them as points and applying a point-pattern matching algorithm. We also measured the reliability of our method as probabilities of true positives and false positives using photographs of various qualities taken at different angles. When we excluded photographs of poor quality and angle the probability of true positives was >80% at a false positive probability of 10%. A new photograph could be preprocessed in <1 min and tested against a reference library of 100 individuals in <10 min. Our computer-aided identification system could be extended for use in other species with variable spot patterns, which could be useful in efforts to estimate various population dynamics parameters essential for the study and conservation of wildlife, particularly threatened and endangered species.