Gene HWP1 encodes a major Candida albicans hyphae cell wall protein which is a substrate of mammalian transglutaminases, promoting the cross-link of the fungus to epithelial cells. Here, we describe a novel HWP1 allele, isolated from C. albicans blood isolates. Analysis of the translated sequence shows that three important regions are absent in the novel allele, HWP1-2, relative to the previously described allele, HWP1-1. Regions 1 and 2 consist of 10 amino acid repeats important for functional conformation of peptide chains and attachment of C. albicans cells to the mammalian epithelia. Region 3 consists of 34 amino acid residues rich in threonine and serine, with O-glycosylation sites that promote the cross-linking with other proteins on C. albicans surface. The HWP1-2 homozygous strain L757 and the heterozygous strain L296 (HWP1-1/HWP1-2) have significantly lower levels of HWP1 expression during hyphal growth and biofilm formation compared to strain SC5314 (HWP1-1/HWP1-1). However, strain L296 properly forms hyphae and biofilms in vitro while strain L757 has reduced hyphal growth (40.4%) and biofilm formation (90.8%). Our results indicate that the HWP1 locus has biofilm specific allelic differential expression and suggest that the HWP1-2 encoded protein is less efficient to maintain cell-to-cell and cell-to-surface adhesion during biofilm formation. This is the first report of a natural variant of HWP1.