Candida dubliniensis is a pathogenic yeast species closely related to Candida albicans. However, it is less frequently associated with human disease and displays reduced virulence in animal models of infection. Here comparative genomic hybridization was used in order to assess why C. dubliniensis is apparently less virulent than C. albicans. In these experiments the genomes of the two species were compared by co-hybridizing C. albicans microarrays with fluorescently labelled C. albicans and C. dubliniensis genomic DNA. C. dubliniensis genomic DNA was found to hybridize reproducibly to 95.6 % of C. albicans gene-specific sequences, indicating a significant degree of nucleotide sequence homology (> 60 %) in these sequences. The remaining 4.4 % of sequences (representing 247 genes) gave C. albicans/C. dubliniensis normalized fluorescent signal ratios that indicated significant sequence divergence (< 60 % homology) or absence in C. dubliniensis. Sequence divergence was identified in several genes (confirmed by Southern blot analysis and sequence analysis of PCR products) with putative virulence functions, including the gene encoding the hypha-specific human transglutaminase substrate Hwp1p. Poor hybridization of C. dubliniensis genomic DNA to the array sequences for the secreted aspartyl proteinase-encoding gene SAP5 also led to the finding that SAP5 was absent in C. dubliniensis and that this species possesses only one gene homologous to SAP4 and SAP6 of C. albicans. In addition, divergence and absence of sequences in several gene families was identified, including a family of HYR1-like GPI-anchored proteins, a family of genes homologous to a putative transcriptional activator (CTA2) and several ALS genes. This study has confirmed the close relatedness of C. albicans and C. dubliniensis and has identified a subset of unique C. albicans genes that may contribute to the increased prevalence and virulence of this species.