Functional extinction is the extinction of a species or other taxon such that:

1. It disappears from the fossil record, or historic reports of its existence cease;
2. The reduced population no longer plays a significant role in ecosystem function; or
3. The population is no longer viable. There are no individuals able to reproduce, or the small population of breeding individuals will not be able to sustain itself due to inbreeding depression and genetic drift, which leads to a loss of fitness.

In plant populations, self-incompatibility mechanisms may cause related plant specimens to be incompatible, which may lead to functional extinction if an entire population becomes self-incompatible. This does not occur in larger populations.

In polygynous populations, where only a few males leave offspring, there is a much smaller reproducing population than if all viable males were considered. Furthermore, the successful males act as a genetic bottleneck, leading to more rapid genetic drift or inbreeding problems in small populations.