Background Insecticide-based interventions play an integral role in malaria vector control. However, the continued spread of insecticide resistance threatens to undermine progress made thus far and may ultimately lead to operational failure of current control measures. Clothianidin and chlorfenapyr both have unique modes of action and have expanded the number of insecticide classes available to vector control programmes. Prior to field use, it is imperative to establish their toxicity against local mosquito populations and evaluate potential cross-resistance with other chemicals used contemporarily or historically. The aim of this study was to determine the diagnostic doses of clothianidin and chlorfenapyr and their efficacies against Anopheles arabiensis , the predominant Ethiopian malaria vector species. Methods A range of doses of clothianidin and chlorfenapyr were tested, using modified WHO susceptibility tests and CDC bottle bioassays, respectively, against an Ethiopian susceptible laboratory strain and a wild population of An. arabiensis collected from Oromia Region, Ethiopia. Cross-resistance to other public health insecticides: carbamates (bendiocarb and propoxur), organophosphate (malathion) and pyrethroids (deltamethrin and permethrin), was assessed in the same mosquito populations using CDC bottle bioassays. Results Complete mosquito mortality was observed with the laboratory strain using the recommended diagnostic doses for clothianidin (2%/filter paper) and chlorfenapyr (100 µg/bottle). The field population was resistant to malathion (83% mortality), capable of surviving 2×, 5× and 10× the diagnostic dose of both deltamethrin and permethrin, but susceptible to bendiocarb and propoxur. The field population of An. arabiensis was significantly more susceptible to clothianidin, reaching 100% mortality by day 2 compared to the laboratory strain (100% mortality by day 3). In contrast, the wild population was less susceptible to chlorfenapyr, with the highest mortality of 99% at 72 h using 200 µg/bottle compared to the laboratory colony, which reached complete mortality at 50 µg/bottle by 24 h. Conclusions The putative diagnostic doses of clothianidin and chlorfenapyr are appropriate for monitoring resistance in An. arabiensis from Ethiopia. The unique modes of action and an absence of cross-resistance render clothianidin and chlorfenapyr potential candidates for inclusion in the National Malaria Control Programme vector control efforts, particularly in areas with high pre-existing or emergent resistance to other insecticide classes.