We sequenced ribosomal DNA intergenic spacer subrepeats and their flanking regions of foxtail millet landraces from various regions in Europe and Asia and its wild ancestor to elucidate phylogenetic differentiation within each of types I-III found in our previous work and to elucidate relationships among these three types. Type I was classified into seven subtypes designated as Ia-Ig based on subrepeat sequences; C repeats downstream of those subrepeats are also polymorphic. Of these, subtypes Ia-Id and Ig were found in foxtail millet landraces. Subtypes Ia and Ib were distributed broadly throughout Asia and Europe. Subtype Ic was distributed in China, Korea and Japan. Subtype Id has a 20-bp deletion in subrepeat 3 and has a unique C repeat sequence. This subtype was found in a morphologically primitive landrace group from Afghanistan and northwestern Pakistan and differed greatly from other type I subtypes, implying that these landraces were domesticated independently. Subtypes Ig was found in a landrace from Pakistan and Ia and Ie-Ig were in six wild ancestor accessions. Type II was also highly polymorphic and four subtypes were found and designated as subtypes IIa-IId, but sequence analyses indicated type III as monomorphic. The present work indicates that type III should be classified as a subtype of type II (subtype IIe). Sequence polymorphism of subrepeats of types I-III indicated that subrepeats of subtype IIa are greatly divergent from others. Relationships among types I-III are much more complicated than anticipated based on previous RFLP work.