North American Castanea consists of three morphologically variable species: Castanea dentata, Castanea pumila, and Castanea ozarkensis. Taxonomy of these species has been complicated by intermediate morphology, similarity in growth habit due, in part, to the chestnut blight, and putative naturally occurring hybridization in the southern Appalachians. The primary goal of this study was to determine if chloroplast DNA (cpDNA) distribution reflects the morphological variation observed in North American Castanea. To that end, we sequenced a single cpDNA gene region for 233 accessions collected from much of the range of the genus in North America. Once samples were grouped into haplotypes, we sequenced additional cpDNA regions to ensure that the observed haplotypic relationships were robust. We identified four main lineages and observed that for three of these, leaf and twig morphology are reliable predictors of haplotype identity (especially outside of the southern Appalachians). Haplotypes of the fourth lineage are shared among accessions of C. dentata and C. pumila, and trees with intermediate morphology. Geographic mapping of the haplotypes showed that they are largely found in separate geographic ranges but overlap in the southern Appalachians. While three clades closely correspond to the morphology of North American Castanea, it appears that the fourth lineage may have been recognized in the past as the hybrid taxon Castanea × neglecta because of its morphology that is intermediate between C. dentata and C. pumila.