Genetic variation of caribou (Rangifer tarandus) at 18 microsatellite DNA loci and the cytochrome-b gene of mitochondrial DNA (mtDNA) was quantified in 11 herds of 3 North American subspecies: Alaskan barren ground caribou (R. t. granti), Canadian barren ground caribou (R. t. groenlandicus), and woodland caribou (R. t. caribou). Phylogenetic analysis of 1,194 nucleotides of cytochrome-b sequence resulted in a clade of 52 genotypes in R. t. granti, R. t. groenlandicus, and in 1 herd of R. t. caribou, and a clade of 7 genotypes in R. t. caribou. mtDNA sequence divergence is approximately 1% between these clades and 0.3–0.6% within these clades. The subspecies do not have monophyletic mtDNA, but do have different frequencies of mtDNA genotypes. Microsatellite allele frequencies also are differentiated between the woodland (R. t. caribou) and barren ground (R. t. granti and R. t. groenlandicus) subspecies. An exception is the George River herd in Labrador, which is classified as R. t. caribou but has mtDNA and microsatellite allele frequencies intermediate between the other herds of R. t. caribou and R. t. groenlandicus. Within subspecies, there is relatively low differentiation of microsatellite allele frequencies and mtDNA genotypes among herds of R. t. granti and R. t. groenlandicus, and relatively high differentiation of microsatellite alleles and mtDNA genotypes among herds of R. t. caribou in 4 geographically separate areas in Canada. The extent of differentiation of mtDNA genotype frequencies and microsatellite allele frequencies within and among each subspecies reflects past and present gene flow among herds. Issues related to subspecies, populations, ecotypes, and herds are discussed.