We studied hybridization and introgression between Black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadees along two transects in the Appalachians using four genetic markers and multivariate analysis of morphology. Genetic data revealed that at least 58% of the birds in the center of each transect were of mixed ancestry and that recombinant genotypes predominated among hybrids, demonstrating that hybridization is frequent and that many hybrids are fertile. Genetic clines generally were steep and coincident in position, but introgression was evident well beyond the range interface. Introgression was higher at the one autosomal locus surveyed than in mitochondrial DNA or in two sex-linked markers, suggesting that the hybrid zone is a conduit for gene flow between the two forms at some loci. On a broad scale, morphometric variation was concordant with genetic variation. Clines in morphological variation based on principal components (PC) scores were steep and coincident with genetic clines. Also, a strong correlation within a population between PC scores and an individual's genetic makeup suggested that a large amount of morphological variation was genetically determined. However, morphological analysis indicated that hybrids were uncommon on one transect, whereas genetic data clearly showed that they were common on both. In addition, patterns of morphological variation were equivocal regarding introgression across the hybrid zone. Thus, genetic data provided a complementary and more detailed assessment of hybridization, largely due to the discrete nature of genetic variation. Genetic markers are useful in understanding hybridization and introgression, but diagnostic markers may underestimate average gene flow if selection against hybrids maintains steep clines at diagnostic loci. To gain a clearer picture of the genome-wide effects of hybridization, a much larger number of loci must be assayed, including non-diagnostic ones.