The African Anopheles funestus and the Asian An. minimus groups are closely related and are probably considered distinct only because of their geographic separation. This study aimed at improving two identification methods based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) already developed for either group. Each PCR-RFLP, either on the internal transcribed spacer 2 (ITS2) for the An. minimus group, and domain 3 (D3) for the An. funestus group, was applied to the other group for the standardization of one identification method applicable on both continents. The ITS2 fragment digested by Bsi ZI showed the highest diagnostic power. This assay allowed the discrimination of at least 13 Anopheles species within the subgenus Cellia from two continents (Africa and Asia), among which are five major malaria vectors. Moreover, digestion of the D(3) with Msp I showed intragenomic variations within An. funestus populations. Two types of D3 copies (M and W) occurred in specimens from southern Africa. The populations from West-Central Africa presented only type W and East-Malagasy populations exhibited type M. Since An. funestus shows a great capacity of adaptation, these molecular variations, along with behavioral and ecologic ones, reinforce the hypothesis of a species complex that will need to be further investigated.