DNA obtained from non- or minimally invasive samples such as scats, hairs, feathers, and shells can be used to monitor individuals in conservation settings, an approach known as ‘molecular tagging’. Non-invasive sampling is favoured over live capture due to the ability to monitor elusive species, as well as minimise human disturbance and eliminate risk of injury or death during live capture. Here we demonstrate the development and applications of ‘molecular tagging’ using scats from one bat and three mammal species (ghost bat, banded hare wallaby, rufous hare wallaby, and bilby). First, we pre-select potential Single Nucleotide Polymorphism (SNP) markers from population genomic data to generate a panel of ~50 SNPs markers for individual identification. Second, DNA is extracted from scats using protocols that handle poor quantity/quality scat DNA. Extracted DNA is then genotyped with the pre-selected SNP panels on the MassArray platform. We can also assign sex to scats using custom-made sexing markers. Lastly, the data generated is processed in our custom-made publicly available R package ‘ScatMatch’ by filtering scat genotypes’ quality, assigning scats to individuals and incorporating other metadata such as GPS locations and sex into the final report. Genetic tagging can reveal spatial and temporal patterns of habitat usage, track hybridization patterns, assess the success of translocations or predator control and can be incorporated into models to estimate abundance (mark recapture) and distribution (species distribution model). Molecular tagging provides a bridge between genetics and ecology and represents a valuable tool in the species monitoring toolkit.