The conodonts first appeared during the Cambrian Stage 2 (also referred as Tommotian).
The still unnamed Cambrian Stage 10 can be defined as the first appearance of Eoconodontus notchpeakensis. The upper boundary is defined as the appearance of Iapetognathus fluctivagus which marks the beginning of the Tremadocian and is radiometrically dated as 485.4 ± 1.9 million years ago.
The Cambrian–Ordovician extinction event occurred approximately 488 million years ago. This early Paleozoic extinction event extirpated many conodonts.
The Lau event, about 420 million years ago, a relatively minor mass extinction during the Silurian period, had a major impact on conodont populations.
The Kačák Event was a period of significant extinctions. The group most affected was the Ammonoidea, although there were also faunal turnovers amongst conodonts and dacryoconarids.
The entire class is postulated to have been wiped out in the Triassic–Jurassic extinction event, which occurred roughly 200 million years ago. Near the end of the Triassic deadly marine biocalcification began to occur, along with oceanic acidification, sea-level fluctuations and the Central Atlantic Magmatic Province (CAMP) releasing carbon dioxide, sulfur dioxide and aerosols. These environmental catastrophes caused the extinction of the conodonts, along with 34% of other marine genera.
The last conodont species to appear, Neohindeodella detrei, existed at the very end of the Rhaetian. The youngest conodont specimen of this species was found in the earliest Hettangian of Hungary, when the final extinction of conodonts occurred.