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Background  Malaria burden is high in Nigeria, yet information on the major mosquito vectors is lacking especially in the Sudan savannah region of the country. In order to facilitate the design of future insecticide-based control interventions in the region, this study has established the resistance profile of  An. gambiae s.l.  populations in two northern Nigeria locations and assessed the contribution of target site resistance mutations.    Methods  Larval collection was conducted in two localities in Sudan savannah (Bunkure and Auyo) of northern Nigeria between 2009 and 2011, from which resulting adult, female mosquitoes were used for insecticides bioassays with deltamethrin, lambda-cyhalothrin, DDT and malathion. The mosquitoes were identified to species level and molecular forms and then genotyped for the presence of  L1014F-kdr ,  L1014S-kdr  and  ace-1   R   mutations.    Results  WHO bioassays revealed that  An. gambiae s.l.  from both localities were highly resistant to lambda-cyhalothrin and DDT, but only moderately resistant to deltamethrin. Full susceptibility was observed to malathion.  An. gambiae , M form (now  An. coluzzii ), was predominant over  An. arabiensis  in Auyo and was more resistant to lambda-cyhalothrin than  An. arabiensis . No ‘S’ form ( An. gambiae s.s .) was detected. A high frequency of 1014 F mutation (80.1%) was found in  An. coluzzii  in contrast to  An. arabiensis  (13.5%). The presence of the 1014 F  kdr  allele was significantly associated with resistance to lambda-cyhalothrin in  An. coluzzii  (OR = 9.85; P < 0.001) but not in  An. arabiensis . The L1014S- kdr  mutation was detected in a single  An. arabiensis  mosquito while no  ace-1   R   mutation was found in any of the mosquitoes analysed.    Conclusions  The predominance of  An. coluzzii  and its resistance profile to main insecticides described in this study can guide the implementation of appropriate vector control interventions in this region of Nigeria where such information was previously lacking.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2334-14-441) contains supplementary material, which is available to authorized users.

High frequency of kdr L1014F is associated with pyrethroid resistance in Anopheles coluzzii in Sudan savannah of northern Nigeria