AbstractBlood samples were collected in Algeria from 4,444 army recruits and tested for 10 genetic polymorphic systems. These samples were collected from territorial Wilayas (administrative units of Algeria) from which the young soldiers had originated. Based on similar geography and economic and political history, these Wilayas were clustered into 10 regions. These regions, not part of the governmental administrative units, were characterized by allelic frequencies, and analyzed using R‐matrix principal components, Wright's FST, spatial autocorrelation, and Mantel tests. Hierarchical relationships between the culturally defined regions were examined using two different analytical methods of phylogenetic tree constructions: neighbor‐joining, and unweighted pair group average arithmetic (UPGMA). These results indicated the predominance of genetic homogeneity due to the gene flow between regions, but with some migration emanating from sub‐Saharan Africa and Mediterranean Europe. Wright's FST value of 0.0063, based on 16 alleles, suggested a relatively small genetic microdifferentiation of the regions. In Algeria, gene flow apparently swamped most of the effects of stochastic processes and disrupted the relationship between geography and genetics, as characterized by the isolation‐by‐distance model. Some genetic differences and similarities were observed between regions or clusters of regions. The resulting genetic structure of the Algerian populations is best explained by a combination of gene flow, ecology, and history. Am. J. Hum. Biol. 18:492–501, 2006. © 2006 Wiley‐Liss, Inc.