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While non-invasive genetic methods have become increasingly important for estimating the abundance of wildlife populations, finding sufficient high-quality samples for accurate genotyping and population estimation remains a challenge. We tested whether salivary DNA from twigs browsed by moose (Alces alces) could complement fecal samples for individual identification and population size estimation using genetic mark-recapture. Browsed twigs and fecal samples were collected from two adjacent plateau mountains in Southern Sweden with a potentially isolated moose population. Twig samples were first genotyped with SNP (single nucleotide polymorphism) assays developed for cervid identification. The moose-positive twig and fecal samples were then genotyped on a SNP assay developed for individual identification. Both sample types generated genotypes of sufficient quality for individual identification and the total population size was estimated to be 37 moose, 95% CI [30, 52]. Average amplification rates of twig samples identified as moose and fecal samples were 0.81 and 0.61, respectively. However, genotyping error rates were relatively high in both sample types and only 10% of twig samples and 35% of fecal samples could be used in population genetic analyses. Amplification rate was not useful for filtering out samples with a high error rate, since some samples displayed high error rates despite 100% amplification. We found that graphical analysis of the distribution of allelic differences between all samples is an efficient way of separating real genetic variation from genotyping errors and for deciding the rate of genotyping errors that can be tolerated when grouping genotypes for individual identification.