To clarify the relationship between the impact of phenological and/or artificial factors on seed quality, we measured the numbers of strobili on nematode-resistant Pinus densiflora clones grown in an immature and relatively small scale (700 m2) seed orchard. In addition, we established the clonal identities of all ramets, identified the paternal parent of the seeds, and assessed the resistance of seedlings to nematode infection. We also clarified the quantitative differences of strobili among clones; one clone produced 86.4% and 70.8% of all male strobili and female strobili, respectively. However, given that the total contamination ratio of the orchard was 82.0%, immigrant pollen had a larger impact on the success of actual crossing than phenology. Seedlings with a resistant maternal parent were resistant, even when their paternal parent was from outside the orchard. Two unselected clones were also planted in the seed orchard, one of which was not resistant and was associated with a maternal contribution of 34.7% of all seed stock. These findings suggest that, despite having a large impact on the crossing, immigrant pollen has a minor impact on seed resistance. Conversely, unselected and nonresistant clones have a marked impact on seed resistance. We concluded that artificial factors have larger impact on the seed quality than phenological factors in this orchard and the seeds will be of sufficient quality for supplying the market once nonresistant clones have been removed from the orchard.