A radiocarbon date of 8900 years before present establishes human presence on San Miguel Island but additional radiocarbon dating may place human occupation on the island as far back as 10,700 years. Archaeological surveys have mapped 542 Indian sites on the island, evidence that occupation on the island was more than casual or temporary. The Chumash Indians called San Miguel Island "Tuqan".

The first European to land on San Miguel Island was Juan Rodriguez Cabrillo, a Portuguese explorer on October 18, 1542. The expedition of Cabrillo discovered and named the islands of San Miguel and Santa Rosa "Islas de San Lucas". He later changed the name of San Miguel Island to "La Posesion" from one of his ships.

It is known that Cabrillo wintered on San Miguel Island in 1542 during which time he broke either an arm or a leg which later became infected. Knowing he was a dying man, Cabrillo turned his expedition over to his chief pilot Bartolome Ferrer. January 3, 1543 Cabrillo died as a result of his injury, and many believe he was buried on the island, although his grave was never found. In 1937 to honor this explorer, the Cabrillo Civic Clubs of California, a statewide Portuguese organization, placed a 40 inch high monument to Cabrillo on a knoll overlooking Cuyler Harbor.

After Cabrillo's death the island was renamed "Juan Rodrigues" or "la Capitana" in his honor. In 1748 it appeared as "San Bernardo" on a map and was adopted by Miguel Costanso on his 1770 map. The name "San Miguel" won acceptance from the charts of English explorer George Vancouver in 1793.

In 1848, the Treaty of Guadalupe Hidalgo ceded California to the U.S. Government but the Channel Islands were not included. The treaty was redrawn a few years later, but San Miguel Island was again inadvertently omitted from the the list of islands the United States was to acquire. In 1895, Great Britain intended to take advantage of this technicality in order to acquire a coaling station between Vancouver and the Hawaiian Islands. President Grover Cleveland must have heard of the threat, for in July, 1896, Nicholas Covarrubias, local U.S. Marshall, had orders to sail with a group of surveyors to appropriate the property. The surveyors completed their work, and the island was assumed by many to be a United States Possession.

As on various other Channel Islands, squatters, fisherman and otter hunters lived on the island during historic times. In the 18th and 19th centuries, sea mammal hunters were drawn to the island in search of the fur bearing sea otter (Enhydra lutris). Yankees, Russian sponsored Aleuts, and Kanakas and others were among those who came to hunt.

Ranching probably began on the island sometime around 1850. The early "owners" of the islands were not legal owners, but owners by possession only. The first record of a long term resident on San Miguel Island was that of George Nidever. George Nidever purchased 6000 sheep, 125 head of cattle and 25 horses and "All the right, title, interest, claim and ownership..." to one half of the island. The sale was made by the Santa Barbara County Sheriff to settle the debts of Samuel C. Bruce. This is the first recorded deed for San Miguel Island. It is unknown how Samuel Bruce obtained his interest.

The  San Miguel Island was bought and sold several times over the next 18 years, when in 1887, one half of the island was sold to William G. Waters for $10,000. Captain Waters was a veteran of the Civil War and a commissioned officer with the Fifteenth Massachusetts. After the war he moved to California and resumed his trade as printer.

In 1888, Captain Waters moved his wife, adopted daughter, maid and ranch hands to the island and began ranching. Captain Waters wife stayed on the island for only a portion of one year. She moved back to the mainland and died the following year. In 1897, Waters formed the San Miguel Island Company with the assistance of investors. In 1908, Waters and investor Elias Beckman became involved in a lawsuit which resulted in the U.S. Government exercising its right of ownership.

Between 1911 and 1948. San Miguel Island saw its share of lessees with the U.S. Government. One of these lessees was Robert Brooks. Brooks hired his long time friend Herbert Lester to help manage the island.  Herbert Lester was a victim of shell shock from World War I. After spending years in an Army hospital, Brooks felt the island would help him.

In 1930, Lester and his wife Elizabeth moved to San Miguel Island. The Lesters lived in the house originally built by Captain Waters and had two daughters on the island. They seldom went to the mainland and when it came time to educate the children, Mrs. Lester did it herself. Herbert Lester became quite proficient in obtaining unusual memorabilia from shipwrecks and had his "Killer Whale Bar" to display them. Lester even proclaimed himself "King of San Miguel". Lester's endless charm and astonishingly likable personality together with Elizabeth's humor and intellect served as a magnet to draw famous and plain people out to the island. It was in 1935 that Mutiny on the Bounty was filmed near the island.

Sadly, Herbert Lester, despondent over his health and ever tightening Navy restrictions, committed suicide in 1942. He was buried above Harris Point on San Miguel Island. His wife Elizabeth raised her children on the mainland. In 1974, Mrs Lester published The Legendary King of San Miguel Island, a history of her life on the island. Elizabeth Lester died in 1981 and is buried next to her husband.

In 1948, the Navy revoked Robert Brook's lease and ordered him off the land within 72 hours. Brooks left behind much of his belongings and livestock. He returned once in 1950 in a short trip to collect some additional items but he was never allowed to collect it all.

Sheep grazed undisturbed until the 1960s when the Navy ordered the elimination of all the animals. In 1966 the last 148 sheep were hunted and eliminated. The island continued to be a central point for naval training well into the 1970's. In 1980, San Miguel Island became part of the Channel Islands National park.