The area around Humboldt Bay was once solely inhabited by the Wiyot Indian tribe. One of the largest Wiyot villages, Tolowot, was located on Gunther Island (AKA Indian Island and AKA Bloody Island) in Humboldt Bay. Founded circa 900, it contains a shell midden 6 acres (24,000 m²) in size and 14 feet (4 m) deep. It was the site of the February 26, 1860 massacre of the Wiyot people that was recorded by Bret Harte, then living in Union, now called Arcata. Between 60 and 200 Wiyot men, women, and children were murdered that night. In 1998, musician Frank Black wrote and recorded a song about this event, called "Humboldt County Massacre." Tolowot is now an archaeological site, designated "Gunther Island Site 67", and is a National Historic Landmark.[2]

State historic landmarks in Humboldt County include Trinidad Head, Fort Humboldt, The Old Arrow Tree, Centerville Beach Cross, Camp Curtis, the Town of Trinidad, the City of Eureka, California's first drilled oil wells in Petrolia, the Jacoby Building, the Old Indian Village of Tsurai in Trinidad, the Arcata and Mad River Railroad Company, the Humboldt Harbor Historical District, and the town of Ferndale.[2]

On February 5 and 6, 1885, Eureka's entire Chinese population of 300 men and 20 women were expelled after a gunfight between rival Chinese gangs (tongs) resulted in the wounding of a 12 year old boy and the death of 56 year old David Kendall, a Eureka City Councilman. After the shooting, an angry mob of 600 Eurekans met and then informed the Chinese that they were no longer wanted in Eureka and would be hanged if they were to stay in town longer than 3 p.m. the next day. They were put on two steamships and shipped to San Francisco. No Chinese were killed in the expulsion. Another Chinese expulsion occurred during 1906 in a cannery on the Eel River, which expelled 23 Chinese cannery workers after local loggers objected to their presence. However, A few Chinese remained in the Orleans area, where some white landowners sheltered and purchased food for Chinese mineworkers until after racial tension passed. The Chinese did not return to the coastal cities until the 1950s.[3]