Myzus persicae and Brevicoryne brassicae are the main aphid pests and vectors of viruses that attack many crops, including oilseed rape, the most commonly grown dicotyledonous crop in the Czech Republic. In this study, we analysed the flight activity of both aphids from five suction traps over 20 years (2004–2023). We focussed on (i) the influence of the ban on seed dressing with neonicotinoids on aphid catches, (ii) the influence of the average temperature on flight activity, and (iii) the number of males/females caught in the suction traps. We compared the data on aphid flight activity at the coldest and warmest sites and found that migration starts about 10 days earlier at the warmest site than at the coldest site and that aphid populations are more numerous here. The number of catches in suction traps was observed for both aphids after the ban on neonicotinoids was significantly increased. For M. persicae, it was about 9 times higher, while for B. brassicae, it was about 1.3 times higher. In addition, we observed a significant decrease in the number of males in M. persicae with a simultaneous increase in the number of females (in autumn), which could be an indication of the formation of anholocyclic populations. Overall, our results showed a significantly high abundance of both aphid species depending on the observed locations, which seems to be related to the ban of neonicotinoids. Therefore, an effective alternative is needed to improve the control of aphid vectors that can ensure the stability of crops against aphid-transmitted virus diseases.