Over 2000 basepairs of mitochondrial DNA (mtDNA) sequences were compared to (1) examine evolution in protein coding versus noncoding [control region (CR)] segments, and (2) test the species-level distinctiveness of the California gnatcatcher (Polioptila californica) and clarify its phylogenetic and biogeographic relationships to other arid-adapted gnatcatchers. Unlike some studies, CR region I (left domain) was not as variable as coding genes. As expected, the central domain of the CR varied little, whereas CR II (right domain) showed high levels of variation. CR sequences tended to be "phylogenetically noisy" as evidenced by lower rescaled consistency indices, relative to those for coding genes. The California gnatcatcher differs from its sister-species, the black-tailed gnatcatcher (P. melanura), by approximately 4.0%, which supports species-level recognition. Two other aridland gnatcatchers, the black-capped gnatcatcher (P. nigriceps) and white-lored gnatcatcher (P. albiloris), are closely related to the previous two species, also at a level of about 4 to 4.5% sequence divergence. These species evolved over a relatively short time, but prior to the most recent Pleistocene glaciations.