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Hybridization plays an important role in the evolution of some of the vertebrate taxa on the Galápagos Islands, such as the Darwin finches. Conversely, only a single possible hybrid between the Galápagos marine iguana (Amblyrhynchus) and the land iguana (Conolophus) has been reported from the island Plaza Sur. In this paper, the hybrid status of a morphologically unusual iguana from this island is confirmed, using restriction fragment length polymorphism (RFLP) analyses of the nuclear ribosomal DNA (rDNA). Sequencing of the hybrid's mitochondrial cytochrome b gene revealed that it was the offspring of a female land iguana and a male marine iguana. Preliminary molecular analyses of morphologically typical marine and land iguanas from Plaza Sur did not detect introgression of nuclear or mitochondrial markers between species. The potential significance of hybridization for the evolution of the Plaza Sur iguana populations is discussed.