There is one near-extinction event that is fairly well-known, although it remains controversial. Roughly 70,000 years ago, give or take a few thousand years, an enormous eruption occurred in what is now Sumatra, leaving behind Lake Toba. The eruption coincides with a population bottleneck that is often cited as the reason for the relatively low genetic diversity across Homo sapiens sapiens. Research suggests as few as 2,000 humans were left alive by the eruption and its aftereffects.
A recent paper in the Proceedings of the National Academy of Sciences found another population bottleneck much farther back in human history. Genetic studies found that 1.2 million years ago there were as few as 55,000 members of genus Homo, including pre-human hominids like Homo erectus and Homo ergaster.