Candida glabrata is an important human pathogen, and an understanding of the genetic relatedness of its clinical isolates is essential for the prevention and control of fungal infections. In this study, we determined the relatedness of 38 Candida glabrata clinical isolates originating from two teaching hospitals in Slovakia. The 14 different genotypes were found by using microsatellite marker analysis (RPM2, MTI and Cg6) and DNA sequencing for analysis of the entire ERG11 gene. Subsequent sequencing of amplified DNA fragments of the PDR1, NMT1, TRP1 and URA3 loci in ten selected clinical isolates revealed identical DNA sequence profiles in five of them. They displayed the same microsatellite marker sizes and contained the same H576Y amino acid substitution recently described in the Pdr1p multidrug resistance transcription factor responsible for azole resistance. These results demonstrate the genetic diversity of C. glabrata clinical isolates in our hospitals and indicate a common clonal origin of some drug resistant ones.