In recent years, the decline of pine stands in Europe, including Poland, has been caused by the emerging needle pathogen Dothistroma septosporum. Although this fungus appears to preferentially infect Pinus pini, P. pinaster or P. radiata in Southern Europe, it has been reported in stands of P. nigra, P. mugo and P. sylvestris from Southern Poland. Our preliminary tests of symptomatic needles of diseased pines, including black pine (P. nigra), showed the presence of both D. septosporum and D. pini—the latter as the first report in Poland. No other endophytic pathogen, i.e., Lecanosticta acicola or Cenangium ferruginosum, were found. More extensive molecular surveying based on β-tub2 amplification of DNA in needle samples from 72 seed trees of P. sylvestris in nine different Forest Districts of Southern Poland did not find the presence of D. septosporum. Our study revealed that the seed trees from which we collected propagation material were free from the pathogen, and its endophytic behavior was not confirmed in our testing. Consequently, these investigated trees of P. sylvestris should be suitable for seed collection and propagation, following the requirements of “good” phytosanitary quality as “pathogen-free” pine seeds used for reforestation.