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Individual marking allows researchers to collect important data using Mark-recapture method. Photographic Identification Method (PIM) has obtained favorable opinions, being effective and less intrusive with respect to traditional marking procedures. Here, we developed and tested the efficacy of a software-aided PIM based on different characteristics, which act as natural marks. Target species were the northern spectacled salamander (Salamandrina perspicillata, Amphibia: Urodela) and the stag beetle (Lucanus cervus, Coleoptera: Lucanidae). We considered as natural mark the ventral pattern of S. perspicillata and, for the first time in L. cervus, the presence/number of small denticles on male mandibles. We selected 4 independent characteristics, each one with several states, for each species. We asked participants, with different degree of familiarity with the species, to identify recaptured individuals through manual PIM. To assess the advantages of the software, we compared the time spent by experts of the species to identify an individual through manual PIM and software-aided PIM. We further compared our semi-automated method with a fully automated one. The software efficiency was calculated by increasing the number of characteristics used to filter individuals from the database (from 1 to 4). The chosen characteristics proved their reliability for individual identification and can be used as natural marks. The proposed software-aided PIM shorten the identification time, does not led to mismatching errors and proved its efficacy regardless of the taxa/characteristic used. Thus, this tool can be consider a more practical alternative to conventional marking techniques, in particular for sensitive and threatened species that need quick and effective monitoring programs carried out with non-invasive sampling methods.