Significance The current rate of species extinction is ∼1,000 times the background rate of extinction and is attributable to human impact, ecological and demographic fluctuations, and inbreeding due to small population sizes. The rate and the initiation date of rapid population decline (RPD) can provide important clues about the driving forces of population decline in threatened species, but they are generally unknown. We analyzed the genetic diversity data in 2,764 vertebrate species. Our population genetics modeling suggests that in many threatened vertebrate species the RPD on average began in the late 19th century, and the mean current size of threatened vertebrates is only 5% of their ancestral size. We estimated a ∼25% population decline every 10 y in threatened vertebrate species.