Habitat destruction and loss can be traced to anthropogenic and nature-wrought causes. Anthropogenic activities include destructive and unsustainable practices such as

1. logging,
2. fires,
3. land conversion,
4. siltation,
5. destructive fishing methods, and
6. encroachment and occupancy in protected areas.

Nature-wrought destructions are due to natural calamities like volcanic eruptions, earthquakes, typhoons, and pests and diseases. The Mt. Pinatubo volcanic eruption has resulted in the loss of undetermine vital components of the tropical forest and marine waters of the Subic-Bataan National Park. It also resulted in the destruction of vast farmlands by its volcanic lava and subsequent lahar flows. Furthermore, agroecosystems that lie along typhoon paths suffer significant destruction annually.

Population pressure, poverty and paucity of livelihood opportunities, dearth of values, and the "open access" nature of many bioresources all contribute to the overexploitation and non-sustainable use of our country’s biodiversity.

In forests, commercial timber species (e.g., dipterocaps, kamagong, narra) as well as non-timber species (e.g., orchids, ferns, rattan, insects, birds, mammals) and animal products (e.g. birds’ nests, guano), are overharvested. Mangrove timber are overharvested for fuelwood, animals for trade (waterfowls, reptiles) and fish and shellfish for food. In the marine ecosystem, commercially important species, notably tuna, shellfish and other edible species are overharvested. Agricultural ecosystems are hard pressed to yield greater harvests to feed the teeming population. Protected areas are not spared the onslaught of overexploitation from the greedy hands of man because of economic realities.

Pollutants overwhelm our ecosystems and overtax the dispersal and self-cleansing capacity of our atmosphere, water bodies and land.

Forest ecosystems, in general, are less subjected to chemical pollution compared to other ecosystems with the exception of chemical defoliants usage. It is the wetland ecosystems that take much toll from chemical wastes from mine tailings, hazardous wastes from industrial plants, factory discharges, agricultural fertilizer and pesticide run-offs, and even household wastes. Marine ecosystems are subject to the same chemical pollutants as wetlands but they are less vulnerable because of their greater expanse. Oil slicks, however, inflict serious harm to marine habitats and their biota. Agricultural ecosystems are poisoned by intensive fertilizer and pesticide applications. Even useful non-pests and humans, as well , are threatened by this inappropriate farming method.

By and large, the successful introduction of exotic species occurred in wetland ecosystems, particularly in lakes and rivers, and has been at the expense of the endemic and indigenous species either directly through predation, competition, and hybridization or indirectly through parasites and habitat alteration. For instance, the original fish population of Caliraya Lake has disappeared with the introduction of the black bass, Microterus salmoides.

Weak Institutional and Legal Capacities

Major drawbacks in biodiversity conservation and sustainable use include:

1. inappropriate, overlapping, conflicting and obsolete policies and institutions,
2. shortage of technical expertise, (iii) shortage of funds,
3. weak information, education, and communication capacities,
4. inadequate policy mechanisms, and (vi) poor integration of research and development activities.