Living modified organisms (LMOs) are managed by seven government agencies according to their use in South Korea. The Ministry of Environment is responsible for LMOs used for environmental remediation. This study aimed to develop guidelines for assessing potential risks posed by transgenic plants used for remediation to insect ecosystems by investigating arthropod communities in sunflower fields. A total of 2,350 insects and spiders belonging to 134 species of 10 orders and 71 families were collected from sunflower fields over four growth stages ranging from anthesis to seed maturity. At the R3 phase of flower-bud formation, Chironomidae sp. of a decomposer insect guild presented the highest density, while Apis mellifera of a pollinator guild was the most abundant in the R5.8 phase of flowering. During the R7 seed-filling phase and the R9 phase of seed maturity, herbivorous Pochazia shantungensis predominated. During the R9 phase, richness and diversity indices of arthropod communities were distinctly lower whereas their dominance indices were significantly higher than those at other phases. In addition, the composition of arthropod communities was strongly correlated not only with the sampling date, but also with the sampling method depending on the growth stage of sunflowers. Our results suggest that appropriate sampling timing and methods should be considered in advance and that long-term field trials that cover a variety of environmental conditions should be carried out to evaluate potential risks to insect ecosystems.