The island scrub jay was first described by American
ornithologist Henry Wetherbee Henshaw in 1886 and an archaeological specimen at site SCRI-192 dating from the 1780s-1812 on Santa Cruz Island is the earliest evidence of the bird in the historic period. but are now considered four species: the
Florida scrub jay (
A. coerulescens), the island scrub jay, the
California scrub jay (
A. californica), and
Woodhouse's scrub jay (
A. woodhouseii).
DNA studies indicate that the island and coastal forms have long been isolated from their relatives inland. The relationships within the genus have been studied in several papers (e.g.) Island scrub jays seem to be incapable of crossing to the mainland. However they were once present on three of California's northern Channel Islands,
San Miguel Island,
Santa Rosa Island, and Santa Cruz Island where they persist today. Reliable historical observer records for island scrub jays in addition to Santa Cruz Island include only a single 1892 account on neighboring
Santa Rosa Island, only about 10 km (6 mi) away. 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. 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, ==Distribution and habitat==