The dataset contains an AFLP Excel Macro (Rinehart 2004) that was used to convert allele size data from GeneMapper4.0 (Applied Biosystems, USA) into binary form and to indicate the presence “1” or absence “0” of MSAP fragments. Only reproducible fragments ranging from 150 to 500 bases were counted and further analyzed in order to reduce the impact of potential size homoplasy (Vekemans, Beauwens et al. 2002). The dataset contains results from 3 natural populations of Taxus baccata from Mt Cholomon, Mt Olympus and Mt Vourinos and their respective individuals.