The apparently sudden appearance of nearly modern flowers in the fossil record initially posed such a problem for the theory of evolution that Charles Darwin called it an "abominable mystery". However, the fossil record has considerably grown since the time of Darwin, and recently discovered angiosperm fossils such as Archaefructus, along with further discoveries of fossil gymnosperms, suggest how angiosperm characteristics may have been acquired in a series of steps. Several groups of extinct gymnosperms, in particular seed ferns, have been proposed as the ancestors of flowering plants, but there is no continuous fossil evidence showing exactly how flowers evolved. Some older fossils, such as the upper Triassic Sanmiguelia, have been suggested. Based on current evidence, some propose that the ancestors of the angiosperms diverged from an unknown group of gymnosperms in the Triassic period (245–202 million years ago). Fossil angiosperm-like pollen from the Middle Triassic (247.2–242.0 Ma) suggests an older date for their origin. A close relationship between angiosperms and gnetophytes, proposed on the basis of morphological evidence, has more recently been disputed on the basis of molecular evidence that suggest gnetophytes are instead more closely related to other gymnosperms.
The evolution of seed plants and later angiosperms appears to be the result of two distinct rounds of whole genome duplication events. These occurred at 319 million years ago and 192 million years ago. Another possible whole genome duplication event at 160 million years ago perhaps created the ancestral line that led to all modern flowering plants. That event was studied by sequencing the genome of an ancient flowering plant, Amborella trichopoda, and directly addresses Darwin's "abominable mystery."
The earliest known macrofossil confidently identified as an angiosperm, Archaefructus liaoningensis, is dated to about 125 million years BP (the Cretaceous period), whereas pollen considered to be of angiosperm origin takes the fossil record back to about 130 million years BP. However, one study has suggested that the early-middle Jurassic plant Schmeissneria, traditionally considered a type of ginkgo, may be the earliest known angiosperm, or at least a close relative. In addition, circumstantial chemical evidence has been found for the existence of angiosperms as early as 250 million years ago. Oleanane, a secondary metabolite produced by many flowering plants, has been found in Permian deposits of that age together with fossils of gigantopterids. Gigantopterids are a group of extinct seed plants that share many morphological traits with flowering plants, although they are not known to have been flowering plants themselves.
In 2013 flowers encased in amber were found and dated 100 million years before present. The amber had frozen the act of sexual reproduction in the process of taking place. Microscopic images showed tubes growing out of pollen and penetrating the flower's stigma. The pollen was sticky, suggesting it was carried by insects.
Recent DNA analysis based on molecular systematics showed that Amborella trichopoda, found on the Pacific island of New Caledonia, belongs to a sister group of the other flowering plants, and morphological studies suggest that it has features that may have been characteristic of the earliest flowering plants.
The orders Amborellales, Nymphaeales, and Austrobaileyales diverged as separate lineages from the remaining angiosperm clade at a very early stage in flowering plant evolution.
The great angiosperm radiation, when a great diversity of angiosperms appears in the fossil record, occurred in the mid-Cretaceous (approximately 100 million years ago). However, a study in 2007 estimated that the division of the five most recent (the genus Ceratophyllum, the family Chloranthaceae, the eudicots, the magnoliids, and the monocots) of the eight main groups occurred around 140 million years ago. By the late Cretaceous, angiosperms appear to have dominated environments formerly occupied by ferns and cycadophytes, but large canopy-forming trees replaced conifers as the dominant trees only close to the end of the Cretaceous 66 million years ago or even later, at the beginning of the Tertiary. The radiation of herbaceous angiosperms occurred much later. Yet, many fossil plants recognizable as belonging to modern families (including beech, oak, maple, and magnolia) had already appeared by the late Cretaceous.