The genetic structure of brown hyena (Hyaena brunnea) populations in any part of their distribution is unknown. Brown hyenas live in clans whose territories and membership change, making nongenetic estimates of population structure and relatedness among individuals difficult to establish. Sixty-one brown hyenas from the west coast of Namibia were genotyped at 10 microsatellite loci designed for the spotted hyena (Crocuta crocuta). We found reduced microsatellite variation in brown hyenas compared to spotted hyenas. Using nonhierarchical analyses we detected no major genetic subdivisions across the area sampled in Namibia, but weak differentiation among 2 clans in the southern portion of the range. Females within clans were significantly more related (r_wc♀♀  =  0.34 ± 0.072 SE) than females between clans (r_bc♀♀  =  0.022 ± 0.033) and than females and males in clans (r_wc♀♂  =  0.058 ± 0.076). Examination of these data indicates that dominant males were not related to dominant females and that there is multiple paternity within clans.