The origin of present day amphibians is still a mystery in contrast to that of the reptiles. In general, fossil records that link the three genera of present day amphibians to the ancient tetrapods are still missing; this is a rather huge gap in the history of terrestrial animals. The earliest known amphibious fossil (genus Triadobatrachus, located in the Madagascar during the mid-Jurassic Period, approximately 230 million years ago) has already exhibited some of the features that resemble frogs; although they still retain short tailed and have a spine that is twice as long as present day frogs. Early amphibians from Poland similar to frogs (genus Czatkobatrachus, only 5 million years younger than Triadobatrachus), provided the evidence that frogs have widely distributed in the Triassic period. The earliest salamander (Marmorerpeton, found in England during middle-Jurassic Period, from 165 million years ago) and caecilians (Eocaecilia, with leg-like appearance, found in Arizona, USA, during Jurassic Period 190 million years ago) have specialized in their own way and have became what they are today. Thus, the first amphibians may have originated at an earlier period, perhaps sometime during the Permian Period, or even earlier.

Incomplete fossil records can only provide limited help. But this also gives rise to several questions regarding how these animals were unable to form fossils easily; fossils of smaller and more fragile organisms, like the offspring of Megalocephalus, with external gills, were found. The reason may have an ecological significance: the ancestors of present day amphibians may settle in very shallow ponds or streams in the mountain which a number of ancient tetrapod species were less likely to be prey upon; and in the same coincidence, the fossils formed in these types of terrain are relatively few. For instance, as we have known, Marmorerpeton is a completely aquatic salamander.

Without key fossil records, the relevance in evolution must be obtained through deductive reasoning by comparing the modern organisms. Through long-term evolution, there is a huge difference between frogs and salamanders and we generally consider the two are the descendants of different families from the ancient tetrapods. Subsequent research proposed that although they have different physical appearances, frogs, salamanders and caecilians have many common basic characteristics, especially: 1. the morphology of skin glands, which shows that skin is used for respiration; 2. The structure of the inner ear and the retina of the eye; 3. distinct pedicellate teeth structure, each tooth is composed of a base secured in the mandible with a replaceable crown attached above.

The possibility that all of these common features were independently evolved is marginal; consequently, after continuous arguments, a more rational explanation is to theorize that they are monophyly. Therefore, most biologists have classified the three groups as class Lissamphibia.