We investigated the impact of watermelon grafted onto Cucumber Green Mottle Mosaic Virus (CGMMV)-resistant transgenic watermelon rootstock on insects as non-target organisms in a greenhouse in 2005. We quantitatively collected insect assemblages living on leaves and flowers, and we used sticky traps to collect alate insects. We compared the patterns of insect assemblages and community composition, cotton aphid (Aphis gossypii Glover) on watermelon leaves and western flower thrip (Frankliniella occidentalis Trybom) on watermelon male flowers, between CGMMV-resistant transgenic watermelon (TR) and non-transgenic watermelon (nTR). Non-parametric multidimensional scaling (NMS) ordination verified that insect assemblages on leaves and sticky traps were different between TR and nTR (P < 0.05). The insect assemblages on male flowers were not statistically significant. Multi-response permutation procedures proofed our results from NMS results (P > 0.05). Conclusively, TR watermelons appear to have some adverse effects on the population of cotton aphids on leaves and sticky traps, but watermelon male flowers do not show an adverse effect. Further research is required to assess the effect of TR on the aphid and western flower thrip. Life table experiments might support the specific reason for the adverse effects from leaf assemblages. Assessment of non-target impacts is an essential part of the risk assessment of non-target insects for the impact of transgenic organisms.