The present publication represents an overview of knowledge pooled by participants at the "Analysis of microsatellite sequences in Scots pine" Workshop organised by the PROFOREST Centre of Excellence. The Workshop was divided into three parts, the first being devoted to the microsatellite analysis performed on Scots pine, the second concerning the use of molecular-marker analyses in different forest tree species and pathogen detection, and the third describing the statistical methods by which genetic data in forestry are analysed.