The shoebill was known to both ancient Egyptians[3] and Arabs,[citation needed] but was not classified until the 19th century, after skins and eventually live specimens were brought to Europe. John Gould described it in 1850, giving it the name Balaeniceps rex. The genus name comes from the Latin words balaena "whale",[4] and caput "head", abbreviated to -ceps in compound words.[5]

Traditionally allied with the storks (Ciconiiformes), it was retained there in the Sibley-Ahlquist taxonomy which lumped a massive number of unrelated taxa into their "Ciconiiformes". More recently, the shoebill has been considered to be closer to the pelicans (based on anatomical comparisons)[6] or the herons (based on biochemical evidence).[7] Microscopic analysis of eggshell structure by Konstantin Mikhailov in 1995 found that the eggshells of shoebills closely resembled those of other Pelecaniformes in having a covering of thick microglobular material over the crystalline shells.[8] A recent DNA study reinforces their membership of the Pelecaniformes.[9]

So far, two fossil relatives of the shoebill have been described: Goliathia from the early Oligocene of Egypt and Paludavis from the Early Miocene of the same country. It has been suggested that the enigmatic African fossil bird Eremopezus was a relative too, but the evidence for that is unconfirmed. All that is known of Eremopezus is that it was a very large, probably flightless bird with a flexible foot, allowing it to handle either vegetation or prey.