Genetic variation provides the foundation for species to survive, reproduce and evolve. Wolf trees are an example that may have a difference genetic background; however, research on the genetics of Scots pine (Pinus sylvestris L.) wolf trees is limited. The objectives were to assess (1) the morphological and genetic differentiation of wolf tree morphotypes in artificially established young commercial Scots pine stands using chloroplast microsatellite (cpSSR) DNA markers; and (2) the genetic differentiation based on progeny testing of mature wolf tree and regular tree morphotypes found in natural Scots pine stands. Our material consisted of (a) a 20-year-old artificially established stand in central Lithuania, where we morphotyped all trees and genotyped 59 wolf trees and 50 control trees at 6 cpSSR loci, (b) a nursery test where we assessed the morphology of 2-year-old open pollinated progeny of 8 wolf trees (20 seedlings per tree) in comparison with a control selected in a mature stand in northwestern Lithuania. Results showed a significant genetic differentiation between wolf trees and regular trees in young plantations based on the cpSSR DNA markers. Wolf trees had a higher genetic diversity at the cpSSR loci compared to the regular trees in the young plantations. The progeny test showed wolf trees contained more lateral shoots and possessed larger crown at age 2 in the nursery test. Our study suggests that there is a genetic background for the morphological differentiation between wolf trees and regular commercial Scots pine trees. However, the morphotype structure of wolf trees is complex, thus requiring future replicated studies spread across different regions and age classes.