The dimorphic yeast Candida albicans is a component of the normal microflora at the mucosal surfaces of healthy individuals. It possesses an array of phenotypic properties considered as virulence traits that contribute to pathogenicity of the yeast in immuno-compromised patients. We addressed the question of the pathogenicity of lineages of C. albicans with regard to their genotype in three series of C. albicans isolates (a series of commensal isolates collected in healthy individuals, a group of bloodstream isolates and a group of non-bloodstream clinical isolates) using a Multi-Locus Microsatellite Typing (MLMT) approach based on the analysis of the polymorphism of 11 microsatellite loci. The MLMT analysis of the three series, corresponding to 174 C. albicans isolates, gave a 100% typability to the method, with a DP index of 0.999. The UPGMA analysis showed that the isolates segregated in eight phylogenetic groups. Interestingly, the clustering was comparable when using NJ and MS-tree algorithms and a good concordance index of the clustering was observed with MLST. All in all our data strongly indicated MLMT as a reliable tool for DNA-typing studies in C. albicans. Isolates from healthy and non-healthy individuals segregated at the same proportions into the eight phylogenetic groups, suggesting that isolates of different origin share the same overall pathogenicity. Surprisingly allelic frequencies at the HIS3 microsatellite differed significantly in commensal isolates (group A) from pooled groups B and C (clinical isolates), raising the possibility that some individual alleles at the HIS3 microsatellite may be associated with distinct pathogenic profiles in C. albicans.