In 1999 the Forest Service of the Government of Navarre set up two experimental sites in Western Pyrenees (Navarra, NE Spain) to study the effect of different thinning intensities over Scots pine (Pinus sylvestris) stands in nine plots (30 x 40 m) per site. From 2000 to 2019 were recorded the species occurrences of vascular plants and bryophytes, and their cover measured in percentage, in ten 2 x 2 m quadrats per plot in both sites. The species checklist of each site is provided, based in the first recorded occurrence, with the geographical coordinates referred to the centroid of each site.