Golden-winged Warblers (Vermivora chrysoptera) and Blue-winged Warblers (V. pinus) are small, brightly colored Neotropical migrant birds that breed in eastern North America. Wherever the two species occur together, they hybridize to a limited degree, producing distinctive hybrid phenotypes. In recent decades, chrysoptera has experienced dramatic population declines across much of its range. Those declines have often been correlated with establishment and increase of pinus in the same areas, but it remains uncertain what, if any, role pinus has played in driving the decline of chrysoptera. In a first attempt at molecular genetic analysis of chrysoptera-pinus population dynamics, Gill (1997) reported cryptic, completely asymmetric, and possibly very rapid introgression of pinus mitochondrial DNA (mtDNA) into chrysoptera, causing what he termed “local cytonuclear extinction” of chrysoptera. As Gill (1997) noted, however, those results were based on relatively small samples from a single area in Pennsylvania. To begin to investigate the generality of Gill’s findings and to establish a baseline for long-term genetic and ecological studies, we intensively sampled one new study area (in southern West Virginia) and also sampled more broadly across two other areas (in Michigan and Ohio) that have experienced pinus invasions and chrysoptera declines. In southern West Virginia, introgression of mtDNA appeared to be roughly symmetrical: 15% (11 of 72) of pinus phenotypes possessed chrysoptera mtDNA, and 12% (17 of 137) of chrysoptera phenotypes possessed pinus mtDNA. Results from much smaller samples from Michigan and Ohio also failed to show any evidence of asymmetric mitochondrial introgression. The results we report here, based on mtDNA and plumage phenotype information for 337 birds representing much of the range of the two species, indicate that previous genetic results and inferences from Pennsylvania may not be broadly applicable to the many areas of contact between chrysoptera and pinus in eastern North America.