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The Candida haemulonii complex (Candida haemulonii, Candida haemulonii var. vulnera, and Candida duobushaemulonii) comprises emerging opportunistic human fungal pathogens with recognized multidrug-resistance profiles. Little is known about the virulence markers produced by this fungal complex. However, it is recognized that Candida spp. express a large array of peptidases, which play multiple roles in different aspects of fungal-host interactions. In the present study, we have identified proteolytic enzymes in clinical isolates of the C. haemulonii complex using zymographic assays. Peptidases able to hydrolyze gelatin, casein, albumin, hemoglobin, and immunoglobulin G were detected in cell-free supernatants and cellular extracts taken from the three species forming the C. haemulonii complex. Overall, peptidases were preferentially evidenced at physiological pH and temperatures of 37–42 °C, with molar masses between 35 and 85 kDa. Peptidase profiles of C. haemulonii and C. haemulonii var. vulnera isolates were quite similar, contrasting to the peptidases produced by C. duobushaemulonii. Almost all peptidases were inhibited by phenylmethanesulfonyl fluoride (PMSF), thus classifying them as serine-type peptidases. Additionally, proteolytic cleavage of soluble azoalbumin was blocked by PMSF (65–95% inhibition depending on the fungal isolate). These unprecedented results have demonstrated the capability of the C. haemulonii complex to produce serine-type peptidases with an ability to cleave a broad spectrum of proteins, including key host components.