Accurate wildlife population density estimates are important for conservation purposes, but can be difficult to obtain where species are elusive or rare. We use individual genotypes derived from hair samples and Spatially Explicit Capture Recapture (SECR) models to estimate the population density of European pine marten (Martes martes) and examine the effects of forest fragmentation on population size. We take the first steps towards linking the number of scats in an area to population density, which may eventually negate the need for expensive genetic analyses in the future. Population density estimates ranged from 0.07 km^-2 (95% CI 0.03-0.16) to 0.38 km^-2 (95% CI 0.11-1.07), which were mid to low compared to other estimates from Scotland. We found support for the previous finding that pine marten density in Scotland increases with forest fragmentation up to a threshold level (20-35% forest cover), beyond which it decreases. We found a non-linear relationship between scat counts and population density, although this relationship may be biased by factors not included in the analysis and should be viewed with caution. Following the recent re-inforcement of pine martens to Wales, non-invasive genetic sampling for population estimation may provide an effective way of monitoring their progress.