The favorable climate of the Mediterranean regions makes these some of the most desirable areas to live. Consequently, there are multiple threats from human activities such as habitat loss and fragmentation from urbanization, agriculture, and recreation. Invasive species of plants and animals are dramatically altering ecosystems and biodiversity in all five regions — often combining with changing fire frequencies to cause vegetation alteration and type conversion. As a result, this ecosystem type (which only occurs on occurs on about three percent of the earth's total land area) is one of the most highly altered on the planet and contains the least undisturbed area of any biome.

Habitate Loss and Fragmentation
The dwindling natural landscape within Mediterranean-type regions is increasingly fragmented by human development interspersed throughout open areas. The fragmentation of natural habitat may jeopardize wildlife populations and provides a point of entrance for non-native, often invasive, plant and animal species. Continued habitat loss and fragmentation threatens the long-term existence of many native species and is one of the greatest threats facing biodiversity in these regions. Larger mammals, such as mountain lions, bobcats, and badgers are particularly at risk, with populations reduced through isolation and habitat loss rendered vulnerable to extinction by chance demographic, environmental, and genetic events.

Invasive Species
Invasive exotic species are a major threat in each of the five Mediterranean ecosystems. The problem is exacerbated by continuing urbanization and increasing recreational use, which contributes to disturbances, including fire. These disturbances facilitate the introduction and spread of alien plants and animals. Specifically in the California Mediterranean region, many of the invasive exotic plants originate in the Mediterranean basin and northern Europe and have demonstrated superior competitive abilities in human-influenced environments. Alien species present a profound threat to the integrity of native communities through displacement of native species, degradation of wildlife habitat, and disruption of ecosystem function. 

Vegetation Alteration and Vegetation Type Conversion
Deforestation, desertification, and other changes to vegetation type continue to be problems in all Mediterranean-type ecosystems. In the California Mediterranean region, the introduction of herbaceous exotics species, particularly annual grasses, has significantly affected vegetation dynamics and fundamentally altered the fire-ecology. Annual grasses increase the potential for fire by changing the type, distribution, and timing of available fuels. When coupled with increasing opportunities for fire starts associated with urbanization, a feedback cycle is introduced that can lower fire return intervals beyond the capacity for native species to recover. Significant species shifts and even complete loss of native vegetation can occur.