The impact of intergenic recombination on the population genetics of plant mitochondrial genomes is unknown. In an effort to study this in the gynodioecious plant Silene vulgaris three-locus PCR/RFLP genotypes (based on the mitochondrial genes atpA, cox1, and cob) were determined for 239 individuals collected from 20 North American populations. Seventeen three-locus PCR/RFLP genotypes were found. Recombination was indicated by observation of each of the four two-locus genotypes possible when the two most common alleles are considered for each of two loci. Based on these common alleles the absolute values of standardized linkage disequilibrium |D′| between pairs of loci range from 0.17 to 0.78. This indicates modest disequilibrium, rather than the maximum value expected in the absence of recombination |D′= 1|, or the linkage equilibrium expected if recombination is pervasive (D′= 0). Values of D′ did not depend on which pair of loci contributed alleles to the analysis. The direction of D′ obtained for the common atpA and cox1 alleles was comparable in sign and magnitude to that obtained by examining similar information obtained in a prior study of European samples. All three loci indicated a high degree of population structure (average F_ST= 0.63), which would limit the within-population genetic diversity required for intergenic recombination to create novel genotypes, if most mating is local. Thus, population structure acts as a constraint on the approach to linkage equilibrium.