[5] This bird is a member of the crow family, and is one of a group of closely related North American species named as scrub jays.

[7] The relationships within the genus have been studied in several papers (e.g.[8]) Island scrub jays seem to be incapable of crossing to the mainland.

[5] The historic observation on Santa Rosa Island is supported by a Pleistocene archaeological record of a single island scrub jay femur from a Late Pleistocene-Holocene site (SRI-V-3) found by Paul Collins of the Santa Barbara Museum of Natural History.

[5] There are also two Late Holocene archaeological remains found in San Miguel Island cave sites.

Early studies suggested that the ancestor of the present population was storm-borne or carried on driftwood to Santa Cruz, or that the colonization occurred during a period of glaciation 70,000 to 10,000 years ago, when sea levels were much lower and the channel between the coast and the islands was correspondingly narrower.

[10] More recent DNA studies show that, although other island endemics such as the island fox and the Santa Cruz mouse may have diverged from their mainland relatives around 10,000 years ago, the scrub jays separated in a period of glaciation around 151,000 years ago.

The most recent analysis indicates that the island scrub jay has been evolving in isolation for approximately one million years,[8] i.e. over multiple glacial cycles.

However, the establishment of West Nile virus (WNV) in southern California in 2003 may pose a threat if it crosses to Santa Cruz Island from the mainland.