The first European explorers to visit Modoc County were the American John C. Frémont and traveling party (including Kit Carson) in 1846.

In 1856, the residents of Honey Lake Valley attempted to secede and form a territory they called Nataqua. After Nevada was granted statehood in 1864, the region of current Modoc County was placed within jurisdiction of Shasta County and Siskiyou County.

In 1864, the Klamath, Modoc and Yahooskin band of the Shoshone signed a treaty ceding lands in both Oregon and California, and the tribes were co-located on the Klamath Reservation.

The Modoc War (or Lava Beds War) of 1872-73 brought nationwide attention to the Modoc. Peace talks in 1873 stalled when they shot and killed General Edward Canby and Rev. Eleazer Thomas.

During World War II, the US government developed several thousand acres just south of Newell as a Japanese American internment camp.

NameNational LandmarkState LandmarkPoint of InterestOther Designation
Fremont's CampN/A6N/AN/A
Bloody PointN/A8N/AN/A
Cressler and Bonner Trading Post, 1865N/A14N/AN/A
Bonner GradeN/A15N/AN/A
Infernam Caverbs Battleground 1867N/A16N/AN/A
Battle of Land's Ranch 1872N/A108N/AN/A
Chimney RockN/A109N/AN/A
Old Emigrant TrailN/A111N/AN/A
Evans and Bailey Flight 1861N/A125N/AN/A
Fort BidwellN/A430N/AN/A
Applegate-Lassen Emigrant Trail (Fandango Pass)N/A546N/AN/A
Tule Lake Relocation Center6000210850.2N/AN/A