In 1871 Bierstadt travelled to California for a two-year visit. The following year he journeyed to the Farallones, a group of rocky islets in the Pacific 26 miles west of the Golden Gate, San Francisco. A lighthouse keeper maintained a home on the otherwise deserted islands, and it is likely that Bierstadt stayed here while he sketched the seal-covered rocks. The present picture was executed following Bierstadt's return in May 1872. Seals on the Rocks is closely related to Farallon Island (Carnegie Institute, Pittsburgh); the prominent rock formation depicted in both works is known as Muir Bridge, or the Natural Bridge.

Seals on the Rocks is one of five major known canvases of this subject. Two of these, Seal Rocks, San Francisco and Seal Rock (Gulf States Paper Corporation, Tuscaloosa, Alabama) also depict Muir Bridge; the other two are Seal Rocks, Farallon Islands (The New Britian Museum of American Art, Connecticut) and Seal Rocks, Farallon Islands.

It is possible that the present painting was lent by Bierstadt in December 1879 to the Brooklyn Art Association Exhibition, no. 4, as Seal Rocks, Golden Gate, California.