We conducted several trials to improve and evaluate an identification technique of mesocarnivore individuals using noseprint photos. Our method used the image analysis software to match a partial noseprint pattern. By comparing flash and non-flash photos of the red fox, Vulpes vulpes schrencki, non-flash photos resulted in higher identification success than did flash photos. Similarity scores, which show the correspondence between reference and check images, were also higher for non-flash photos. A searching image size of 30 × 30 pixels was more effective than larger searching image. The noseprint method yielded high similarity scores and success rates in the identification of individuals of four mesocarnivore species: the red fox, Vulpes vulpes schrencki (n = 42); the raccoon dog, Nyctereutes procyonoides albus (n = 10); the Japanese sable, Martes zibellina brachyura (n = 17); and the masked palm civet, Paguma larvata (n = 12). Identification rates for the same individual from all photos of the same species were 95.2% for the red fox, 100.0% for the raccoon dog, 94.4% for the Japanese sable, and 91.7% for the masked palm civet. The identification of mesocarnivore individuals using noseprint photos is easy and a possible method to use in field studies.