The amount of standing genetic diversity found in oak coppice forests has been subjected to intense debate amongst forest ecologists and managers. In this study, the level of vegetative propagation and the genetic diversity found in a coppice forest of rebollo oak (Quercus pyrenaica) was examined. The current range of rebollo oak in the Iberian Peninsula reveals its adaptation to sub-Mediterranean mountain ecosystems. High sprouting capability, mainly by root suckers, has favoured traditional exploitation of rebollo oak in coppice forests. Using nine microsatellite loci, we have detected 14 clone assemblies compounded by 2–4 stems (7.9 ± 1.3 ramets per genet, considering stand density) and covering an average surface of 11.4 m2 per genet. The levels of genetic diversity and the amount of unique genotypes were high (D = 0.9972, G/N = 0.86) and similar to the clonality levels found in a nearby open oak woodland. Despite numerous clear-cutting rotations, known at least since 1750, and the heavy root sprouting observed after a thinning event, low clonal propagation (∼27%) was detected. This fact pointed towards the long-term persistence of several small clonal assemblies in this coppice. Our findings suggest that intense thinning practices are unadvisable in the conversion of Q. pyrenaica coppice into high forest due to the significant losses of genetic diversity when removing unique genotypes.