The European pine marten (Martes martes) is a species of considerable conservation interest in Britain due to its rarity and status as a recovering native carnivore. In recent years, there has been increased application of non-invasive genetic sampling methods in population studies of Martes species. We investigated the effect of sample source (hair and faeces) in the non-invasive assessment of the distribution, population size and density of pine martens in the Fleet Basin in Galloway Forest, southwest Scotland. Fifty-two hair samples and 114 scats were collected during September and October 2014. Genetic analysis was used to identify the species, gender and individual genotype of samples. There was a significant difference in the genotyping success rate for hair samples (43 %) and scat samples (24 %). In total, 15 individual pine martens were identified; 7 males and 8 females. Capture-recapture programme Capwire produced a population size estimate of 18 individuals (95 % CI 15 to 25). Of the 15 individuals sampled, 14 (93 %) were detected from scat sampling and 5 (33 %) were detected from hair sampling. The population density estimate for a post-breeding population was 0.13 to 0.15 pine martens per square kilometre which is towards the lower limit of densities reported for pine martens elsewhere in Scotland. Data from the study highlight that future non-invasive studies aiming to determine pine marten population size and density should incorporate the collection of both hair and scat samples in order to detect as many individuals within the population as possible.