The northern spotted owl (Strix occidentalis caurina) is a threatened subspecies and the California spotted owl (Strix occidentalis occidentalis) is a subspecies of special concern in the western United States. Concern for their continued viability has arisen because of habitat loss caused by timber harvesting. The taxonomic status of the northern subspecies has been the subject of continuing controversy. We investigated the phylogeographical and population genetic structure of northern and California spotted owls with special reference to their region of contact. Mitochondrial DNA (mtDNA) control region sequences confirmed the existence of two well-differentiated lineages connected by a narrow hybrid zone in a region of low population density in north central California. Maximum-likelihood estimates indicated bidirectional gene flow between the lineages but limited introgression outside the region of contact. The lengths of both the mtDNA hybrid zone and the reduced density patch were similar and slightly exceeded estimates of natal dispersal distances. This suggests that the two subspecies were in secondary contact in a hybrid zone trapped by a population density trough. Consequently, the zone of interaction is expected to be geographically stable. We discovered a third, rare clade of haplotypes, which we interpreted to be a result of incomplete lineage sorting; those haplotypes result in a paraphyletic northern spotted owl with respect to the California spotted owl. A congeneric species, the barred owl (Strix varia), occasionally hybridizes with spotted owls; our results indicated an upper bound for the frequency of barred owl mtDNA haplotypes in northern spotted owl populations of 3%.