In a collection of 395 independent clinical isolates classified as Candida parapsilosis on a biochemical profile basis, 20 Candida metapsilosis strains were identified by molecular tests with an isolation frequency of 5%. Isolates were screened for their susceptibility to conventionally used antifungals and for virulence determinants, such as biofilm formation and protease production. Molecular characterization of C. metapsilosis independent isolates by amplified fragment length polymorphism (AFLP) revealed a high percentage of polymorphic bands. Statistical analysis of the pairwise genetic distances and bootstrapping revealed that recombination occurs and significantly contributes to C. metapsilosis genetic population variability. No association between specific AFLP markers and drug resistance or other phenotypes was observed.