The concept of biosphere reserves was proposed by “the United Nations Educational, Scientific, and Cultural Organization” under “the Man and the Biosphere Program” in 1971. With the spatial structure of functional zoning features, biosphere reserves break the traditional closed protection of nature reserves, becoming an open system. In terms of its spatial structure, a typical biosphere reserve should include three functional areas:

1. Core Protected Area: Every biosphere reserve can include one or more core areas. The core area is strictly protected according to a specific conservation purpose, representing the typical ecosystem of a biogeographic region. As generally an undisturbed or minimally disturbed ecosystem, the core area is not only an important zone for biodiversity conservation, but also a working area for research and monitoring.
2. Special Protected Area: With the aim of making the core area strictly protected, it is usually surrounded by a buffer zone, which is similar in shape to the core area. Within buffer zones, some activities compatible with conservation purposes of the core area, such as research, environmental education, environmental monitoring, training, and ecotourism, can be conducted. It is also acceptable to conduct a few activities that do not affect the utilization of protected resources.
3. Scenic Area: The transition area surrounds the core area and the buffer zone. The residents in the transition area are closely linked to those around the protected area. Experiments, research, traditional land use, etc. can be conducted in this area.

At this stage, the planning of Penghu Marine Geopark is based on the concept of the whole area of Penghu. The core area includes the current nature reserves, wildlife refuges and natural monuments. The management of protected areas is governed by the current regulations; natural monuments will be designated in accordance with the criteria of “Regulations for Designation and Revocation of Natural Landscapes and Natural Monuments” and comply with the relevant regulations. Both of them have a more stringent status of landscape conservation. The environmental education zone is planned to include natural landscapes and important natural landscapes and incorporate the surrounding community as the industrial development zone. Based on the ecological and cultural resources of the local place, a geopark combining the cultural and natural environment has been created and is consistent with the planning and direction of global geoparks.

Penghu Marine Geopark is currently divided into the following areas (click to see details):
＊The core area encompasses the columnar basalt nature reserve, seabird refuge, green turtle nesting refuge and natural monuments.
＊The environmental education zone encompasses natural landscapes, important natural landscapes and wetlands of national importance.
＊The industrial development zone is the residential area and surrounding waters around the environmental education zone.