Recently, researchers have recognized that genetic variation in foundation species influences community structure of associated organisms. The majority of these studies have employed a common garden approach. However, this approach might result in overestimating the importance of genetic variation for shaping associated communities due to excluding environmental and spatial variability. In this study, we examined to what extent genetic variation in a foundation tree explains the structure of arthropod communities in the field, comparing with spatial, temporal, and environmental factors. In continuous mixed forest, we investigated arthropod communities on mature alders. We found that arthropod communities varied with genetic distance of alders based on 1077 SNPs. A generalized dissimilarity model indicated that genetic distance was the most important factor to explain variation of arthropod communities. Among five functional groups, carnivore insects were well correlated with genetic distance of alders. This study supports that the genetic similarity rule would be primarily prominent in community assembly of plant-associated arthropods.