We've discussed before how endangered species are at risk from the increased likelihood of inbreeding, which leads to unhealthy offspring. There's another danger to letting the numbers of animals in a given species become too low. It's called genetic drift.
Genetic drift is the term biologists use to describe the gradual loss of certain genes from a species, genes that may have been very important for that species' survival.
How can animals lose genes? It's kind of like reaching into a bag of M&Ms. If you take out a hundred M&Ms you are sure to get all the colors at least once. If you only take out ten, you may well miss a color. If by chance you haven't missed a color, try it again. Very soon you will come up with, say, no reds.
Every time animals mate, their offspring receives a mixed bag of genes, half from its mother and half from its father. If the father and the mother share many of the same genes, their offspring will receive doubles of some of them. The doubles don't help, and they mean that some other gene that could have been passed on wasn't. Think of the M&Ms. At the point where you failed to pull a red out of the bag, you have lost one gene. If your mate doesn't have that gene either, then your descendants will never have it.
Low populations of animals means less genetic variation, which means genetic drift is more likely. If the gene that gets lost was critical to the survival of the species, they might begin dying off altogether.