Despite over 30 years of deployment, varieties with the Bph3 gene for resistance to the brown planthopper (BPH), Nilaparvata lugens (Stål) (Hemiptera: Delphacidae), are still effective in much of the Philippines. In the present study, we determined the effects of adaptation to one resistant variety, IR62 – assumed to possess the Bph3 gene – on (1) resistance against a series of varieties with similar biotypical responses (presumed to contain the same major resistance genes), and (2) a differential variety with the bph4 gene that occurs at the same chromosome position as Bph3. We also examined the effects of high soil nitrogen on the effectiveness of Bph3. Feeding, planthopper biomass, and development times were reduced in a wild BPH population when reared on IR62 compared with the susceptible standard variety TN1. However, nitrogen application increased the susceptibility of IR62. After 13 generations on IR62, BPH had adapted to the plant’s resistance. Virulence of the adapted BPH against the variety ‘Rathu Heenati’ supports the idea that Bph3 is present in IR62. Across similar IR varieties (IR60, IR66, IR68, IR70, IR72, and IR74), feeding, planthopper biomass, and development rates were generally higher for IR62-adapted than for non-adapted BPH; however, contrary to expectations, many of these varieties were already susceptible to wild BPH. Fitness was also higher for IR62-adapted BPH on the variety ‘Babawee’ indicating a close relation between Bph3 and bph4. The results indicate that the conventional understanding of the genetics behind resistance in IR varieties needs to be readdressed to develop and improve deployment strategies for resistance management.