Assessment of resistance to DDT and permethrin insecticides and molecular detection of knockdown resistance (kdr) alleles were conducted in three populations of Anopheles arabiensis from eastern Sudan. Bioassay mortalities ranged from 96.9% to 99.6% for 4% DDT and from 98.4% to 100% for 1% permethrin. The L1014F and L1014S alleles were detected in 25 of 498 mosquitoes. The overall kdr frequencies ranged from 7.0% in the area where insecticide-treated nets were used to 3.0% in the area with agricultural insecticide use. The presence of the kdr alleles in An. arabiensis in Sudan emphasizes the need to develop appropriate resistance monitoring and management strategies for An. arabiensis.