Prehistory

Penghu 1, a fossil jaw (mandible) dating to the late Pleistocene that belonged to a member of an extinct hominin species, was discovered in the Pescadores Channel around 2008.

Finds of fine red cord-marked pottery at Guoye, Huxi, indicate that Penghu was visited by Austronesians from southwestern Taiwan around 5,000 years ago, though not settled permanently.

Han Chinese from southern Fujian began to establish fishing communities on the islands in the 9th and 10th centuries, and representatives were intermittently stationed there by the Southern Song and Yuan governments from around 1170.

Wang Dayuan gave a detailed first-hand account of the islands in his Daoyi Zhilüe (1349).

Ming dynasty

In the 15th century, the Ming ordered the evacuation of the islands as part of their maritime ban. When these restrictions were removed in the late 16th century, legal fishing communities were re-established on the islands. These fishermen worshipped at the Mazu Temple that gave Magong its name and themselves gave rise to the Portuguese and English name Pescadores. The Ming established a permanent military presence starting in 1597.

At this time, the Dutch East India Company was trying to force China to open a port in Fujian to Dutch trade and expel the Portuguese from Macau. When the Dutch were defeated by the Portuguese at the Battle of Macau in 1622, they seized Penghu, built a fort there, and threatened raids on Chinese ports and shipping unless the Chinese allowed trading with them on Penghu and that China not trade with Manila. In response, the Chinese governor of Fujian demanded that the Dutch withdraw from Penghu to Taiwan, where the Chinese would permit them to engage in trade. The Dutch continued to raid the Fujian coast between October 1622 and January 1624 to force their demands, but were unsuccessful. In 1624, the new governor of Fujian sent a fleet of 40–50 warships with 5,000 troops to Penghu and expelled the Dutch, who moved to Fort Zeelandia on Taiwan.

Qing dynasty

For a period in the mid-17th century, Taiwan and the archipelago were ruled by the Koxinga kingdom (Kingdom of Tungning), which was overthrown by the Qing dynasty in 1683 after the Battle of Penghu.

The Penghu archipelago was captured by the French in March 1885, in the closing weeks of the Sino-French War, and evacuated four months later. The Pescadores Campaign was the last campaign of Admiral Amédée Courbet, whose naval victories during the war had made him a national hero in France. Courbet was among several French soldiers and sailors who succumbed to cholera during the French occupation of Penghu. He died aboard his flagship Bayard in Makung harbour on 11 June 1885.

Empire of Japan

Towards the end of the First Sino-Japanese War, having defeated the Qing in northern China, Japan sought to ensure that it obtained Penghu and Taiwan in the final settlement. In March 1895, the Japanese defeated the Chinese garrison on the islands and occupied Makung. The Japanese occupation of Penghu, with its fine harbor, gave the Imperial Japanese Navy an advanced base from which their short-range coal-burning ships could control the Taiwan Straits and thus prevent more Chinese troops from being sent to Taiwan. This action persuaded the Chinese negotiators at Shimonoseki that Japan was determined to annex Taiwan, and, after Penghu, Taiwan and the Liaodong Peninsula had been ceded to Japan in the Sino-Japanese Treaty of Shimonoseki in April, helped to ensure the success of the Japanese invasion of Taiwan in May.

Penghu County was then called the Hōko Prefecture by the Japanese government of Taiwan. During World War II, Makō (Makung) was a major base for the Imperial Japanese Navy and the embarkation point for the invasion of the Philippines.

Republic of China

In the Cairo Declaration of 1943, the United States, the United Kingdom and China stated it to be their purpose that "all the territories that Japan has stolen from the Chinese, such as Formosa and The Pescadores, shall be restored to the Republic of China". On 26 July 1945, the three governments issued the Potsdam Declaration, declaring that "the terms of the Cairo Declaration shall be carried out". However, the United States and the United Kingdom have regarded the aforementioned documents as merely wartime statements of intention with no binding force in law.

Following the surrender of Japan on 2 September 1945, Supreme Commander of the Allied Powers Douglas MacArthur issued General Order No. 1, which directed Japanese forces to surrender to the Allied Powers and facilitate the occupation of Japanese territories by the Allied Powers. In the Treaty of San Francisco, signed in 1951 and coming into effect in 1952, Japan renounced sovereignty over Taiwan and Penghu, but left their final disposition unsettled. The archipelago has been administered by the Republic of China since 1945.

Boat people fleeing Vietnam in the 1970s and 1980s who were rescued by Taiwan's ships in the South China Sea were sent to Penghu.

On 25 May 2002, China Airlines Flight 611, a Boeing 747-200 aircraft flying from Taipei to Hong Kong, disintegrated and exploded over the Islands. The wreckage slammed into the Taiwan Strait, a couple of miles off the coast. All 225 passengers and crew on board were killed.

Penghu County has a dry-winter humid subtropical climate (Köppen climate classification: Cwa), bordering on a regular humid subtropical climate (Köppen climate classification: Cfa).