Monotremes have been considered by some authors to be members of Australosphenida, a clade that contains extinct mammals from the Jurassic and Cretaceous of Madagascar, South America, and Australia, but this categorization is disputed and their taxonomy is under debate.

In common with marsupials, monotremes lack the connective structure (corpus callosum) which in placentals is the primary communication route between the right and left brain hemispheres.

Some recent work suggests that monotremes acquired this form of molar independently of placentals and marsupials,[6] although this hypothesis remains disputed.

As in all true mammals, the tiny bones that conduct sound to the inner ear are fully incorporated into the skull, rather than lying in the jaw as in non-mammalian cynodonts and other pre-mammalian synapsids; this feature, too, is now claimed to have evolved independently in monotremes and therians,[9] although, as with the analogous evolution of the tribosphenic molar, this hypothesis is disputed.

[10][11] Nonetheless, findings on the extinct species Teinolophos confirm that suspended ear bones evolved independently among monotremes and therians.

[15] This feature, along with some other genetic similarities with birds, such as shared genes related to egg-laying, is thought to provide some insight into the most recent common ancestor of the synapsid lineage leading to mammals and the sauropsid lineage leading to birds and modern reptiles, which are believed to have split about 315 million years ago during the Carboniferous.

This venom is derived from β-defensins, proteins that are present in mammals that create holes in viral and bacterial pathogens.

[16] It is thought to be an ancient mammalian characteristic, as many non-monotreme archaic mammal groups also possess venomous spurs.

All five extant species show prolonged parental care of their young, with low rates of reproduction and relatively long life-spans.

[32][33] Monotremes may have less developed thermoregulation than other mammals, but recent research shows that they easily maintain a constant body temperature in a variety of circumstances, such as the platypus in icy mountain streams.

[36] During the course of evolution, the monotremes have lost the gastric glands normally found in mammalian stomachs as an adaptation to their diet.

[43] 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 placentals, 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.

[44][45][46] 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 placentals.

Teinolophos like modern monotremes displays adaptations to elongation and increased sensory perception in the jaws, related to mechanoreception or electroreception.

[60] Biochemical and anatomical evidence suggests that the monotremes diverged from the mammalian lineage before the marsupials and placentals arose.

[64] In 2024, a prominent assemblage of early monotremes was described from the Cenomanian deposits (100–96.6 Ma) of the Griman Creek Formation in Lightning Ridge, New South Wales.

The extant platypus genus Ornithorhynchus in also known from Pliocene deposits, and the oldest fossil tachyglossids are Pleistocene (1.7 Ma) in age.