In two very closely related but reproductively isolated mite species, Tetranychus urticae and T. turkestani, we found nucleotide diversity to be extensive for mitochondrial DNA (mtDNA) cytochrome oxidase 1 (COI) (3-4%) but extremely reduced for nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS2) (less than 0.5%). By contrast, ITS2 was shown to evolve much faster than COI between species of this genus. Furthermore, we found that these two species are polyphyletic for mtDNA but monophyletic for rDNA. Thus it appears that despite its biparental transmission and multiplicity of copies in the genome, nuclear rDNA has a smaller effective population size than mtDNA in these species. The conjunction of efficient concerted evolution and/or gene conversion in the rDNA cluster, the haplodiploidy of these species and their female-biased sex ratio could account for this apparent contradiction.