We illustrate how molecular-genetic markers help to better understand population processes in the context of the latter's history and the landscape in which they take place. In the Western Capercaillie Tetrao urogallus populations of the Swiss Alps, extensive genotyping using non-invasively sampled faeces and feathers revealed historical gene flow within and among regional occurrences, while the comparison with museum specimens showed the loss of one formerly frequent allele during the 20^th century, representing diversity reduction owing to genetic drift. Estimates based on genotyping gave higher population sizes than those taken from direct and indirect evidences of Capercaillie presence assessed by thorough field work. A time series of one model population (Schwägalp) demonstrated a positive trend in population size over six years, which we consider a consequence of the conservation measures taken in this area and/or of favourable breeding conditions in the year 2003. We highlight the added value of molecular-genetic data, in combination with information from the field and habitat analyses, to increase the effect of conservation measures for the vulnerable Capercaillie as a model species for rare, elusive animal species.