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Background  Progress made in the control of malaria vectors globally is largely due to the use of insecticides. However, success in the fight against malaria has slowed down or even stalled due to a host of factors including insecticide resistance. The greatest burden of the disease is felt in Africa, particularly Nigeria. Unfortunately, adequate information on insecticide resistance is lacking in many parts of the country, particularly the South-East Zone. Hence, this study aims to bridge the information gap in the Zone.    Methods  The study was conducted from April to December 2016.  Anopheles gambiae  ( s.l .) larvae and pupae were collected from one community each, in the five states of the South-East Zone and reared to the adult stage. The adults were subjected to bioassays for insecticide resistance in accordance with the World Health Organization test procedures, across the four classes of insecticides used in public health. The mosquitoes were also subjected to molecular identification to the species level, and genotyped for West African knockdown resistance mutation (L1014F) and insensitive acetylcholinesterase-1 resistance mutation (G119S).    Results  The mosquitoes were susceptible (100%) to bendiocarb but resistant to pirimiphos-methyl (39.6%), deltamethrin (57%) and dichlorodiphenyltrichloroethane (DDT) (13%). Molecular analysis revealed that only  An. gambiae  ( sensu stricto ) was found in all the states except for Ebonyi, where only  Anopheles coluzzii  was present. High frequencies (0.6–0.9) of the L1014F mutation were found across the zone. The L1014F mutation was significantly higher in  An. gambiae  ( s.s .) than in  An. coluzzii  ( P  < 0.0001). A relatively low frequency (0.2) of the G119S mutation was found in  An. coluzzii , and only in Ebonyi State.    Conclusion  The results show that mosquitoes collected from the South-East Zone of Nigeria were resistant to all insecticides used, except for bendiocarb. The presence of L1014F and G119S resistance mutations reported in this study calls for urgent attention to stop the growing threat of insecticide resistance in the country.

Resistance status of Anopheles gambiae (s.l.) to four commonly used insecticides for malaria vector control in South-East Nigeria