Photographic identification is a promising marking technique alternative to the toe-clipping, since it is completely harmless, cheap, and it allows long time identification of individuals. Its application to ecological studies is mainly limited by the time consuming to compare pictures within large datasets and the huge variation of ornamentation patterns among different species, which prevent the possibility that a single algorithm can effectively work for more than few species. Scales of Reptiles offer an effective alternative to ornamentations for computer aided identification procedures, since both shape and size of scales are unique to each individual, thus acting as a fingerprint like ornamentation patterns do. We used the Interactive Individual Identification System (I3S) software to assess whether different individuals of two species of European lizards (Podarcis muralis and Lacerta bilineata) can be reliably photographically identified using the pattern of the intersections among pectoral scales as fingerprints. We found that I3S was able to identify different individuals among two samples of 21 individuals for each species independently from the error associated to the ability of the operators in collecting pictures and in digitizing the pattern of intersections among pectoral scales. In a database of 1043 images of P. muralis collected between 2007 and 2008, the software recognized 98% of recaptures within each year, and 99% of the recaptures between years. In addition, 99% and 96% of matches were ranked among the top five, and no more than 5 minutes were needed for digitizing and processing each image. The lepidosis of reptiles is a reliable alternative to ornamentation patterns in photographic identification of reptiles, which can be effectively analysed using the I3S software. This result represents a significant improvement in photographic identification of reptiles since (i) this procedure can be easily extended to most other species of reptiles, (ii) all kind of individuals within a species can be marked (i.e., young, subadults and adults) despite the differences in ornamentation patterns, and (iii) it is the only technique for species, like the western green lizard, which lack a clear ornamentation pattern.