The genetic structure and relationships among 18 local Southwest European beef cattle breeds (10 from Spain, five from Portugal and three from France) have been inferred from 16 DNA microsatellite loci, by using F-statistics, for conservation purposes. Level of apparent breed differentiation is considerable and multilocus FST values indicate that around 6.8% of the total genetic variation could be explained by breed differences and the remaining 93.2% by differences among individuals. For countries of origin, the French breeds were those that showed a higher genetic uniformity. All breeds, except the Portuguese breeds Barrosã and Mirandesa, showed a significant heterozygotes deficit. Several factors that could cause this deficit are discussed, and the within-population inbreeding estimates obtained are compared with those from genealogical data. Gene flow could have played an important role for genetic uniformity in populations of narrow geographical vicinity. Neither isolation by distance and hierarchical structure associated with geography are detected. However, in sight of the obtained results, we suggest the genetic drift as the most important factor of genetic differentiation among the analysed populations. The apparent taxonomic distinctiveness of the breeds could be, in an important way, the result of a random drift, which can affect the genetic distances among populations.