A study based on 28 microsatellite loci was performed on 32 isolates of Plasmodium falciparum from Pointe Noire (Republic of the Congo) and compared with a cosmopolitan sample of 21 isolates collected from different countries in Africa, Latin America, and Asia. The Pointe Noire population exhibited very high genetic diversity (A = 7.8 +/- 2.6, He = 0.79 +/- 0.11). Significant linkage disequilibria were observed in 28 of 378 pairs of microsatellite loci. This result could be explained by two non-exclusive hypotheses: 1) uniparental propagation (i.e., selfing), leading to non-panmictic associations, and/or 2) a Wahlund effect (i.e., spatial population genetic heterogeneity). These observations are in agreement with data previously obtained from isozyme loci of the same isolates, but contrast with other population genetic analyses conducted in other hyperendemic zones.