Genetic erosion (also known as genetic depletion or genomic erosion) is any decrease in genetic diversity, both naturally occurring and human-caused. The term is sometimes used in a narrow sense, such as when describing the loss of particular alleles or genes, as well as being used more broadly when referring to the loss of a phenotype or whole species.

Genetic erosion occurs because each individual organism has a unique genome; if the individual dies without the chance to breed, any unique genes they carry are lost before they can be passed down to offspring. Two factors that compound and accelerate genetic erosion are habitat loss and habitat fragmentation–often brought on by development of agricultural and infrastructural areas–and low genetic diversity. Low genetic diversity is linked to inbreeding and a weak immune system both of which can then "fast-track" that species towards eventual extinction.

By definition, endangered species suffer varying degrees of genetic erosion. Many species benefit from a human-assisted breeding program to keep their population viable,^{[citation needed]} thereby avoiding extinction over long time-frames. Small populations are more susceptible to genetic erosion than larger populations.

The gene pool of a species or a population is the complete set of unique alleles that would be found by inspecting the genetic material of every living member of that species or population. A large gene pool indicates extensive genetic diversity, which is associated with robust populations that can survive bouts of intense selection. Meanwhile, low genetic diversity (see inbreeding and population bottlenecks) can cause reduced biological fitness and increase the chance of extinction of that species or population.

With genetic erosion being a broad concept, there are several ways in which it can occur. Most tie back to the loss of individuals in a population and therefore a loss of their specific set of alleles. In large numbers, this is referred to as a population bottleneck–caused by various events including human activity and natural disasters–which greatly shrinks the gene pool and leaves fewer and fewer fertile mating pairs.

In addition to being a direct cause, population size also increase the likelihood of genetic erosion with smaller populations being at higher risk. For example, if an individual in a population dies, the chances of the alleles it carried appearing elsewhere in the population are greater in a larger population. Another contributing factor is restriction of gene flow. Without an appropriate amount of dispersal between populations, small occurrences of genetic erosion within one population may be difficult to bounce back from.

All of these factors came into play for one commonly studied example of genetic erosion: the Ngorongoro Crater lions. High prey density is limited to within the crater due to human activity in the surrounding areas. This creates a barrier that prevents dispersal and limits gene flow. The population of lions also experienced several bottlenecks in the last several hundred years both by hunting and disease. Most notably was an epizootic outbreak that reduced the population to only 15 individuals in 1962. These circumstances greatly reduced the genetic diversity within the population leading to various consequences.

The genetic implications can be illustrated by considering the analogy of a high-stakes poker game with a crooked dealer. Consider that the game begins with a 52-card deck (representing high genetic diversity). Reduction of the number of breeding pairs with unique genes resembles the situation where the dealer deals only the same five cards over and over, producing only a few limited "hands".