Anopheles funestus is one of the major malaria vectors in southern Africa and several populations in this region are resistant to pyrethroids. The current study uses a microarray based approach to identify genes up-regulated in the pyrethroid resistant population, FUMOZ, from Mozambique. As the full set of detoxification genes in A. funestus are unknown, this study investigated the utility of the Anopheles gambiae ‘detox chip’ to screen for differentially expressed detoxification genes in A. funestus. Differential expression of detoxification genes in 3 day old adult females and males from the FUMOZ resistant strain and the FANG susceptible strain was identified using the A. gambiae ‘detox chip’. After optimization of the hybridization conditions, over 90% of the probes showed a positive signal. Only three genes were significantly (p < 0.001) differentially expressed in the females, CYP6P9 (5.4-fold), COI (2.7-fold) and CYP6M7 (1.8-fold). The same genes were also significantly differentially expressed in the adult males, CYP6P9 (6.0-fold), COI (2.9-fold) and CYP6M3 (3.6-fold) together with an additional 21 transcripts. Quantitative PCR (qPCR) analysis was conducted to validate the microarray results. This study demonstrated that heterologous hybridization is a helpful tool in identifying detoxification genes differentially expressed in A. funestus strains.