The origin of bats is poorly understood. Fossil remains are meager, but from the fossils that have been found, 30 fossil genera representing 11 families have been identified, and 37 living genera have been discovered in the fossil record. The fossil record extends back to the early Eocene era, about 60 million years ago, and has been documented on five continents - Europe, Africa, Asia, North America, and South America. As fossils, bats are relatively well represented - but interestingly enough, the best examples are also the oldest! These fossils have been assigned to the suborder of Microchiroptera, and appear to be as complex as the order is today, indicating that they “got their evolution right the first time”!

It is suspected that bats originated in the early Paleocene or mid Cretaceous era (70 to 100 million years ago). It is accepted that Megachiroptera evolved independent of Microchiroptera. Undoubtedly, their origin and evolution revolved around the origin of the wing. There have been three evolutions of wings among terrestrial vertebrates: pterosaurs (reptiles), birds (Aves), and bats (Mammals). The pterosaur wing is perhaps most similar to that of a bat! Other similarities include marked body shortening; involvement of the hind limb in the flight membrane; use of dorsal and ventral thoracic muscles to operate the wing; and various modifications of the tail.

Bats are thought to be the descendants of small quadrupedal and arboreal insectivores, such as shrews, moles, and hedgehogs. But there is controversy to this notion since these living insectivores are highly specialized and bear little resemblance to bats. It is most likely that these insectivores share a common ancestor, and are therefore closely related.

Evidence supporting parallel evolution of Mega and Micro Chiroptera include the fact that dentition is not even remotely similar between the two suborders. Megachiroptera teeth are very specialized for eating fruit, totally dissimilar to the various Microchiropteran. The Megachiroptera share a number of special features with the Primates, which are not shared with the Microchiroptera. These include various aspects of the brain and central nervous system; musculature; skeletal system; circulatory system; and reproductive system. The Frugivorous dentition of megachiropterans is more readily derived from early Primates that were also arboreal. Scientists are all but convinced however, that Megachiroptera are NOT Primates, and there are only a few hold outs to the notion.

Echolocation also provides a lot of unanswered questions in the evolution of bats. Acoustic orientation is produced using the larynx, and is very sophisticated. It is exclusive to the Microchiroptera. There are only three species of Megachiroptera that use a crude system of clicks, but they do not use the larynx; they click the rear portion of their tongues instead. These include the Rousettus, and perhaps Epomophorus (6 species of the Epaulette bats). Other mammals that appear to posses echolocation skills include some insectivores (shrews), young mice, and cetaceans (whales and dolphins). More about echolocation will be found in the section dealing with this subject.