There were hundreds of small tribes of Native Californians, with diverse cultures and languages. Most Native Californian tribes were decimated by disease and the stress of their virtual enslavement by the Spanish Missionaries. Later the Americans hunted down and exterminated many of the remaining tribes without mercy. Some were completely wiped out with little trace, such as the Esselen of Big Sur. Others survived adversity and remain active today, particularly some of the tribes in the Northwest coast.
However, a great volume of detailed and accurate information on their culture, mythology and religion is available. This is thanks to pioneering anthropologists at the end of the 19th and beginning of the 20th centuries. Many of these scholars were affiliated with the University of California.
Religion of the Indians of California
by A. L. Kroeber. University of California Publications in American Ethnography and Ethnology (UCPAAE) Vol. 4, No. 6, pp. 319-356. 
Kroeber, who taught at the University of California at Berkeley, is best known for his study of Ishi, described as 'the last wild Indian' (see Yana Texts). He was also the father of the science fiction writer Ursula LeGuin.
Indian Myths Of South Central California.
By A. L. Kroeber. UCPAAE Vol. 4 No. 4, pp. 167-250. .
This covers the mythology of the Costanoans, today known as the Ohlone, who lived in the San Francisco and Monterey Bay area; and the Yokuts, who lived in the San Joaquin Valley.
Myths of the Miwok
By Edward Winslow Gifford. UCPAAE Vol. 12, No. 8, pp. 283-338. 
The Miwok lived in the area which is today Yosemite National Park.
The Dawn of the World
Myths and Weird Tales Told by the Mewan [Miwok] Indians of California, by C. Hart Merriam 
by Roland B. Dixon, Publications of the American Ethnological Society, vol. IV 
The Maidu inhabited the central Sierra Nevada.
by Pliny Earle Goddard. UCPAAE Vol. 1 No. 2 
The Hupa lived in Northwestern California, Humboldt County, on the Trinity River.
by Edward Sapir UCPAAE Vol. 9 No. 1, pp. 1-235. 
The Yana lived in the north-east Sacramento Valley. The most famous Yana was Ishi, 'the last wild Indian'. He is the subject of an excellent book by Theodora Kroeber, wife of Alfred Krober, Ishi in Two Worlds.
Achomawi and Atsugewi Tales and Achomawi Myths
by Roland B. Dixon
JAFL Vol. 22, no. 81, pp. 159-77  and
JAFL Vol. 23, no. 85, pp. 283-7 .
The Achomawi and Atsugewi lived in north-eastern California.
by Friar Geronimo Boscana; tr. by Alfred Robinson; 
This is one of the few ethographic accounts of Native Californian religion from the Mission era. This describes the Juaneños of Mission San Juan Capistrano.
The Mythology of the Diegeños
by Constance Goddard Du Bois, The Journal of American Folk-Lore (JAFL) Vol. XIV, No. 54, pp. 181-5 
A Saboba Origin-Myth
by George Wharton James; JAFL Vol. XV, No. 61, pp. 36-9 
The Legend of Tauquitch and Algoot
by George Wharton James; JAFL Vol. XVI, No. 62, pp. 153-9 
The Story of the Chaup; A Myth of the Diegueños
by Constance Goddard Du Bois; JAFL Vol. XVII, No. 67 pp. 217-42 
This is an article about the mythology of the Diegueño people, who lived in the vicinity of San Diego.
Mythology of the Mission Indians
by Constance Goddard Du Bois; JAFL Vol. XVII, No. 66. p.. 185-8 ; Vol. XIX. No. 72 pp. 52-60 and 73. pp. 145-64. .
This is an article about the mythology of the Luiseño people, who lived to the north of San Diego.
Two Myths of the Mission Indians
by A. L. Kroeber; JAFL Vol. XIX, No. 75 pp. 309-21 
Ceremonies and Traditions of the Diegueño Indians
by Constance Goddard Du Bois; JAFL XXI, No. 82 pp. 228-36 .