Western Scrub-Jays (Aphelocoma californica) range throughout the western United States and Mexico and exhibit substantial geographic variation in morphology and behavior. Western Scrub-Jays are a polytypic species complex with three distinct groups (californica, woodhouseii, and sumichrasti) associated with geography and distinguished by morphology, genetics, and behavior. Until recently, the Island Scrub-Jay (A. insularis) and the Florida Scrub-Jay (A. coerulescens) were considered subspecies within the Western Scrub-Jay complex. We analyzed mitochondrial DNA sequences (control region I) to reveal the phylogenetic relationships within Western Scrub-Jays and used maximum likelihood, a Bayesian approach, and a relaxed phylogenetic approach to construct phylogenies. In addition, we used several methods to estimate divergence time between clades. Our results reveal that the interior woodhouseii group, which contains the sumichrasti subclade, and the coastal californica group have had a long and independent evolutionary history. However, samples from a contact zone in western Nevada were genetically woodhouseii and morphologically californica. Island Scrub-Jays evolved from the coastal californica, which makes Western Scrub-Jays paraphyletic with respect to Island Scrub-Jays. To solve the problem of paraphyly and to more accurately define the diversity that exists within Western Scrub-Jays, we suggest splitting Western Scrub-Jays into two or three species, California Scrub-Jay (A. californica), Woodhouse's Scrub-Jay (A. woodhouseii), and, potentially, Sumichrast's Scrub-Jay (A. sumichrasti).