Brachiopods form one of very few phyla that have been present on Earth for over 550 million years, since early Cambrian times, when the first widespread appearance of animals with mineralized skeletons occurred. They were the most abundant filter-feeding group for much of that time, and dominate fossiliferous deposits in many localities.

Brachiopods are still present in all of the oceans, but are common and abundant only in restricted areas, such as the deep sea, fiords, polar seas, some parts of New Zealand, and the west coast of North America. They also are often found in cryptic habitats (areas which provide protection from physical disturbance and include crevices, underwater caves, and deep rocky overhangs). Many of the temperate and tropical shallow sea localities where they were formerly dominant are now occupied by bivalve mollusks. Whether this replacement is due to competition or whether bivalves more successfully colonized space made available after the dramatic decline of the brachiopods, during the mass extinction event at the end of the Permian period 150 million years ago, is strongly debated. In some areas, however, they still dominate local sites, with densities sometimes exceeding 1000 individuals per square meter.