structural:expansion, information:filtering
Taxonomy

The traditional " Theria hypothesis" states that the divergence of the monotreme lineage from the Metatheria (marsupial) and Eutheria (placental) lineages happened prior to the divergence between marsupials and placental mammals, and this explains why monotremes retain a number of primitive traits presumed to have been present in the synapsid ancestors of later mammals, such as egg-laying. Most morphological evidence supports the Theria hypothesis, but one possible exception is a similar pattern of tooth replacement seen in monotremes and marsupials, which originally provided the basis for the competing " Marsupionta " hypothesis in which the divergence between monotremes and marsupials happened later than the divergence between these lineages and the placental mammals. Van Rheede (2005) concluded that the genetic evidence favors the Theria hypothesis, and this hypothesis continues to be the more widely accepted one.

Monotremes are conventionally treated as comprising a single order Monotremata. The entire grouping is also traditionally placed into a subclass Prototheria, which was extended to include several fossil orders, but these are no longer seen as constituting a group allied to monotreme ancestry. A controversial hypothesis now relates the monotremes to a different assemblage of fossil mammals in a clade termed Australosphenida, a group of mammals from the Jurassic and Cretaceous of Madagascar, South America and Australia, that share tribosphenic molars. However, in a 2022 review of monotreme evolution, it was noted that Teinolophos, the oldest (Barremian ~ 125 million years ago) and the most primitive monotreme differed substantially from non-monotreme australosphenidans in having five molars as opposed to the three present in non-monotreme australosphenidians. Aptian and Cenomanian monotremes of the family Kollikodontidae (113–96.6 ma) have four molars. This suggests that the monotremes are likely to be unrelated to the australosphenidan tribosphenids.

The time when the monotreme line diverged from other mammalian lines is uncertain, but one survey of genetic studies gives an estimate of about 220 million years ago, while others have posited younger estimates of 163 to 186 million years ago (though the already eutherian Juramaia is dated to 161–160 million years ago). Teinolophos like modern monotremes displays adaptations to elongation and increased sensory perception in the jaws, related to mechanoreception or electroreception.

Molecular clock and fossil dating give a wide range of dates for the split between echidnas and platypuses, with one survey putting the split at 19–48 million years ago, but another putting it at 17–89 million years ago. It has been suggested that both the short-beaked and long-beaked echidna species are derived from a platypus-like ancestor.

The precise relationships among extinct groups of mammals and modern groups such as monotremes are uncertain, but cladistic analyses usually put the last common ancestor (LCA) of placentals and monotremes close to the LCA of placentals and multituberculates, whereas some suggest that the LCA of placentals and multituberculates was more recent than the LCA of placentals and monotremes.