Faecal non-invasive genetic sampling is one of the most practicable, ethical and applied tools to investigate the biology and the ecology of elusive or endangered mammal populations. However, the reliability, accuracy and effectiveness of this technique may be deeply conditioned by several factors such as climate, habitat characteristics, seasonality, sample freshness and storage conditions. In this study, we compared the practicality, efficiency, safety and cost-effectiveness of two preservation methods widely applied to collect and preserve wolf excremental DNA: scats in 96% ethanol and faecal swabs in ATL lysis buffer, to be genotyped in non-invasive monitoring projects. Forty-six wolf faecal samples were collected using both storage methods in three different areas of the Central-Northern Italy during two seasonal (cold and hot) periods and their DNAs were genotyped at 12 unlinked autosomal microsatellites through a multiple-tube approach. Genotyping performances and error rates obtained from the two methods resulted not significantly different. Nonetheless, faecal swabs showed to be more practical, safer and cost-effective than ethanol for the collection and analysis of faecal samples. Our study, though conducted on a limited sample size, suggests that faecal swabs could represent a reliable alternative tool to routinely apply in non-invasive genetic projects to monitor the presence, distribution and dynamics of populations of elusive and endangered mammal species such as the Italian wolf, still threatened by illegal poaching, hybridization and conflicts with human activities.