Background Chemical control has been the most efficient method in mosquito control, the development of insecticide resistance in target populations has a significant impact on vector control. The use of agricultural pesticides may have a profound impact on the development of resistance in the field populations of malaria vectors. Our study focused on insecticide resistance and knockdown resistance (kdr) of Anopheles arabiensis populations from Northern Sudan, related to agricultural pesticide usage. Results Anopheles arabiensis from urban and rural localities (Merowe and Al-hamadab) were fully susceptible to bendiocarb 0.1% and permethrin 0.75% insecticides while resistant to DDT 4% and malathion 5%. The population of laboratory reference colony F189 from Dongola showed a mortality of 91% to DDT (4%) and fully susceptible to others. GLM analysis indicated that insecticides, sites, site type, and their interaction were determinant factors on mortality rates (P < 0.01). Except for malathion, mortality rates of all insecticides were not significant (P > 0.05) according to sites. Mortality rates of malathion and DDT were varied significantly (P < 0.0001 and P < 0.05 respectively) by site types, while mortality rates of bendiocarb and permethrin were not significant (P >0.05). The West African kdr mutation (L1014F) was found in urban and rural sites. Even though, the low-moderate frequency of kdr (L1014F) mutation was observed. The findings presented here for An. arabiensis showed no correlation between the resistant phenotype as ascertained by bioassay and the presence of the kdr mutation, with all individuals tested except the Merowe site which showed a moderate association with DDT (OR= 6 in allelic test), suggesting that kdr genotype would be a poor indicator of phenotypic resistance. Conclusion The results provide critical pieces of information regarding the insecticide susceptibility status of An. arabiensis in northern Sudan. The usage of the same pesticides in agricultural areas seemed to affect the Anopheles susceptibility when they are exposed to those insecticides in the field. The kdr mutation might have a less role than normally expected in pyrethroids resistance; however, other resistance genes should be in focus. These pieces of information will help to improve the surveillance system and The implication of different vector control programs employing any of these insecticides either in the treatment of bed nets or for indoor residual spraying would achieve satisfactory success rates.