Two DNA-based methods, the restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR), were used to identify mosquitoes of the Anopheles gambiae Giles complex collected in Kenya. Field-collected specimens of An. gambiae, An. arabiensis Patton, and An. merus Donity were tested. From a sample of 208 mosquitoes, 181 (87%) were identified by the RFLP method and 205 (99%) were identified by the PCR method. There was complete concordance between the two methods with regard to species identification. PCR assays were simpler, faster, and more reliable than RFLP assays.