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Being one of Sweden’s most important tree species, both as a keystone species and for the forest industry, it is important that we keep our stands of Norway spruce (Picea abies (L.) Karst.) as healthy as possible. With an unclear starting point of existing genetic diversity in natural forests we need to both evaluate what levels of natural diversity we have to begin with and how modern forestry practices might affect this. Previous studies have used relatively few markers to study this or similar situation before. We proved that both capture probes and genotyping by sequencing (GBS) show similar results in common diversity measurements and offers many SNPs, although capture probes showed slightly more diversity in the results, we choose to use PoolSeq and GBS together to examine a large number of planted and natural stands of Norwegian spruce in northern Sweden. In line with previous results on the subject we did not find any large differences between our young, planted forests and our old forests, suggesting that today’s re-planting methods have not affected the general diversity in different stands. However, we did find a difference in the variance of our summary statistics on a stand level between planted and old stands, an indicator that there is a possibility that forestry can cause long-term effects. This becomes even more important in the light of possible clonal deployment of Norway spruce. I believe that more research is needed over both larger geographical areas and with a focus on within stand variation. Using mitochondrial and chloroplast DNA to discern finer details of spatial distribution within stands and looking closer at the genotypic diversity within natural and planted stands. An effort should also be put into examine how these possible differences are affecting the rest of the ecosystem, living with and among Norway spruce.