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Evolutionary tree showing the divergence of modern species from their common ancestor in the centre. The three domains are coloured, with bacteria blue, archaea green and eukaryotes red.

More recently, evidence for common descent has come from the study of biochemical similarities between organisms. For example, all living cells use the same basic set of nucleotides and amino acids. The development of molecular genetics has revealed the record of evolution left in organisms' genomes: dating when species diverged through the molecular clock produced by mutations. For example, these DNA sequence comparisons have revealed that humans and chimpanzees share 98% of their genomes and analysing the few areas where they differ helps shed light on when the common ancestor of these species existed.

Prokaryotes inhabited the Earth from approximately 3–4 billion years ago. No obvious changes in morphology or cellular organisation occurred in these organisms over the next few billion years. The eukaryotic cells emerged between 1.6 and 2.7 billion years ago. The next major change in cell structure came when bacteria were engulfed by eukaryotic cells, in a cooperative association called endosymbiosis. The engulfed bacteria and the host cell then underwent coevolution, with the bacteria evolving into either mitochondria or hydrogenosomes. Another engulfment of cyanobacterial-like organisms led to the formation of chloroplasts in algae and plants.

Phylogenetic and symbiogenetic tree of living organisms, showing a view of the origins of eukaryotes and prokaryotes

The history of life was that of the unicellular eukaryotes, prokaryotes and archaea until about 610 million years ago when multicellular organisms began to appear in the oceans in the Ediacaran period. The evolution of multicellularity occurred in multiple independent events, in organisms as diverse as sponges, brown algae, cyanobacteria, slime moulds and myxobacteria. In 2016 scientists reported that, about 800 million years ago, a minor genetic change in a single molecule called GK-PID may have allowed organisms to go from a single cell organism to one of many cells.

Soon after the emergence of these first multicellular organisms, a remarkable amount of biological diversity appeared over a span of about 10 million years, in an event called the Cambrian explosion. Here, the majority of types of modern animals appeared in the fossil record, as well as unique lineages that subsequently became extinct. Various triggers for the Cambrian explosion have been proposed, including the accumulation of oxygen in the atmosphere from photosynthesis.

About 500 million years ago, plants and fungi started colonising the land. Evidence for the appearance of the first land plants occurs in the Ordovician, around 450 million years ago, in the form of fossil spores. Land plants began to diversify in the Late Silurian, from around 430 million years ago. The colonisation of the land by plants was soon followed by arthropods and other animals. Insects were particularly successful and even today make up the majority of animal species. Amphibians first appeared around 364 million years ago, followed by early amniotes and birds around 155 million years ago (both from "reptile"-like lineages), mammals around 129 million years ago, homininae around 10 million years ago and modern humans around 250,000 years ago. However, despite the evolution of these large animals, smaller organisms similar to the types that evolved early in this process continue to be highly successful and dominate the Earth, with the majority of both biomass and species being prokaryotes.

Estimates on the number of Earth's current species range from 10 million to 14 million, of which about 1.2 million have been documented and over 86 percent have not yet been described.