Previous microsatellite analysis (Barr et al. 2008) of the endangered Black-capped Vireo (Vireo atricapilla) revealed a low (F_ST = 0.021) but statistically significant level of population differentiation with isolation by distance (IBD); most pairwise F_ST values among populations were significant. No clear geographic pattern was detected, although populations in Oklahoma were somewhat differentiated, as expected from the observed pattern of IBD. Because nuclear loci, including microsatellites, coalesce more slowly than mtDNA, we sequenced the mitochondrial ND2 gene for 108 individuals sampled from breeding populations in Oklahoma, Texas, and Mexico to determine whether there was a clearer geographic pattern than that resolved by the microsatellite allele-frequency data. We obtained an F_ST value of 0.024 (P = 0.08), confirmed IBD, but also did not detect geographic structuring in the haplotype network. The authors of the microsatellite study suggested that the significant F_ST value indicated that populations were not currently connected by gene flow and that the greater attention should be given to dispersal behavior when considering the species' population dynamics. We suggest that the unstructured haplotype network reveals that the Black-capped Vireo can be managed without regard for genetic distinctiveness. That is, we contend that statistical significance of the microsatellite F_ST value has been inappropriately equated with biological significance. We believe that a gene-tree approach, emphasizing reciprocal monophyly, is more appropriate when assessing genetic subdivisions in a species that might then merit special conservation concern.