Systemic candidosis is the most common invasive fungal infection and it is usually caused by Candida albicans or Candida glabrata. Recently, the echinocandin class of antifungal agent, which includes micafungin (MCF), has been added to clinicians' armamentarium. The echinocandins target the synthesis of beta-1,3 glucan, an essential component of the fungal wall, by inhibiting beta-1,3 glucan synthase non-competitively. Although fungal echinocandin resistance is not yet a major clinical problem, resistant Candida isolates have been reported. Objectives: The aim of this study was to investigate the mechanisms of echinocandin resistance in C. albicans, which is diploid, and in C. glabrata, which is haploid. Methods: Genes encoding beta-1,3 glucan synthase (GSC1 and GSL1 in C. albicans, and FKS1 and FKS2 in C. glabrata) from MCF-resistant C. albicans and C. glabrata clinical isolates obtained from patients with echinocandin treatment failure, were sequenced. Mutations discovered in these genes were then introduced singly, and in combination, into the corresponding genes in echinocandin-sensitive laboratory strains. The effects of these mutations on MCF sensitivity were measured. Results: MCF resistance in a C. albicans isolate was associated with a GSC1 mutation affecting amino acid S645. When the S645F mutation was introduced into one GSC1 allele it conferred intermediate echinocandin resistance. When the mutation was introduced into both GSC1 alleles (homozygous mutation) it conferred high-level echinocandin resistance. An MCF-resistant C. glabrata strain had point mutations in both FKS1 and FKS2. The introduction of the FKS2 mutation (premature stop codon) alone had no effect on echinocandin susceptibility, and the FKS1 mutation S629P conferred intermediate resistance. Introduction of both mutations in the same strain conferred high-level echinocandin resistance. Conclusion: Two mutation events are required in both C. albicans and in C. glabrata in order to confer high-level echinocandin resistance. This may explain the low prevalence of echinocandin-resistant fungal isolates.