It was granted in 1842 by Governor Juan B. Alvarado to Juan Avila. The rancho was named for a local Indian village called "Niguili." The grant extended along the Pacific coast from Laguna Canyon and Laguna Beach, past Aliso Creek to Dana Point and San Juan Creek. The rancho encompassed those present-day places and Laguna Niguel, Aliso Viejo, and Laguna Hills.
Juan Avila (1812–1889) was the son of Antonio Ygnacio Avila, grantee of Rancho Sausal Redondo. In 1832, Juan Avila married Maria Soledad Thomasa Capistrano Yorba (–1867). He and Soledad Yorba de Avila had three children who survived to adulthood: Rosa Modesta, who married Pablo Pryor; Guadalupe who married Marco Forster; and Manuel Donanciano who married Delfina Rodriguez. Marco Forster (1839–1904) was the son of John (Don Juan) Forster, owner of the adjacent Rancho Trabuco and Rancho Misión Vieja. Juan Avila was granted the three square league Rancho Niguel in 1842. He was a "judge of the plains" at Los Angeles in 1844, and justice of the peace at San Juan Capistrano in 1846.
With the cession of California to the United States following the Mexican-American War, the 1848 Treaty of Guadalupe Hidalgo provided that the land grants would be honored. As required by the Land Act of 1851, a claim for Rancho Niguel was filed with the Public Land Commission in 1852, and the grant was patented to Juan Avila in 1873.
Juan Avila retained ownership of Rancho Niguel until 1865, when after the droughts of 1863-64, he sold the property to John Forster. Soledad Yorba de Avila died of smallpox in 1867. Rancho Niguel passed from John Forster to Marco Forster to Lewis Moulton and his partner, Jean Pierre Daguerre, who obtained it in 1895.
Lewis Fenno Moulton (1854–1938), the son of J. Tilden Moulton and Charlotte Harding Fenno, was born in Chicago, and after his father's death, the family moved to Boston. In 1874 Moulton came to California via Panama. He worked on Rancho San Joaquin, and subsequently went into the sheep raising business for several years. After his first purchase in 1895 of Rancho Niguel (which adjoined Rancho San Joaquin), additional property was acquired and eventually the ranch consisted of 22,000 acres (89 km2).
Jean Pierre Daguerre (1856–1911), a native of Hasparren, France, came to Los Angeles in 1874 with the French Basque Amestoy family and worked on the Amestoy's ranch near Gardena. In 1882, Daguerre formed a partnership with Marco Forster. In 1886, Daguerre married Maria Eugenia Duguet, who came from France on the same boat as Daguerre. After dissolving the partnership with Marco Forster, Daguerre formed a partnership with Lewis Moulton, and owned a one-third interest in Rancho Niguel.
Historic sites of the Rancho
- Juan Avila Adobe. 
- Ogden Hoffman, 1862, Reports of Land Cases Determined in the United States District Court for the Northern District of California, Numa Hubert, San Francisco
- Diseño del Rancho Niguel
- Spanish and Mexican Ranchos of Orange County
- Portrait of Dona Delfina Rodrigues de Avila
- Samuel Armor, 1921, History of Orange County, California, pp.330, Historic Record Co., Los Angeles
- United States. District Court (California : Southern District) Land Case 130 SD
- Report of the Surveyor General 1844 - 1886
- Samuel Armor, 1921, History of Orange County, California, p. 239, Historic Record Co., Los Angeles
- Samuel Armor, 1921, History of Orange County, California, pp.306-311, Historic Record Co., Los Angeles
- Juan Avila Adobe