Patterns of genetic structure in eusocial naked mole-ratpopulations were quantified within and among geographicallydistant populations using multilocus DNA fingerprinting andmitochondrial DNA (mtDNA) sequence analysis. Individuals withincolonies were genetically almost monomorphic, sharing the samemtDNA control region haplotype and having coefficients of bandsharing estimated from DNA fingerprints ranging from 0.93 to0.99. Family analysis of a hybrid captive colony of naked mole-rats with increased levels of genetic variability usingmultilocus DNA fingerprinting gave results consistent withMendelian inheritance, and has revealed for the first time thatmultiple paternity can occur. In a survey of wild colonies fromEthiopia, Somalia and locations in northern and southern Kenya,we have examined mtDNA control region sequence variation in 42individuals from 15 colonies, and together with multilocus DNAfingerprinting and mtDNA cytochrome-b sequence analysis inselected individuals have shown that these populations showconsiderable genetic divergence. Most of the variance insequence divergence was found to be between geographicallocations (Phi(ct) = 0.68) and there was a significantcorrelation between sequence divergence and geographicalseparation of haplotypes. Six colonies from Mtito Andei insouthern Kenya shared the same control region haplotype,suggesting a recent common maternal ancestor. In contrast, outof four colonies at Lerata in north Kenya, three haplotypeswere identified, and phylogenetic analysis suggests that thisarea may be a zone where two distinct lineages are in closeproximity. Genetic distances were maximal between Ethiopian andsouthern Kenyan populations at 5.8% for cytochrome-b, and areapproaching interspecific values seen between otherBathyergids.