Cap1p, a transcription factor in Candida albicans, is thought to participate in oxidative stress tolerance, but the pathways involved are still unclear. The study was designed to reveal the possible pathways by examining changes in the transcription profile after H2O2 treatment with both the cap1-deleted strain CJD21 and its parental strain CAI4 using microarray analysis. Of the identified 89 genes differentially expressed in CAI4 after exposure to H2O2, 76 genes were in a Cap1p-dependent expression pattern. We have shown that Cap1p is involved in the oxidative stress response in C. albicans via multiple pathways, including the cellular antioxidant defense system (e.g., thioredoxin reductase, glutathione reductase, glutathione S-transferase), carbohydrate metabolism and energy metabolism (e.g., glucose-6-phosphate dehydrogenase, transaldolase, glyoxalase I, NADH-dependent flavin oxidoreductase), protein degradation (e.g., 26S proteasome regulatory subunit, ubiquitin-specific protease), ATP-dependent RNA helicase (e.g., DEAD box protein ATP-dependent RNA helicase), and resistance pathways (e.g., multidrug resistance protein, ABC transporter essential for cadmium resistance). Real-time reverse transcription-PCR analysis further confirmed the results of microarray. Collectively, this study provides new insight into the biological functions of Cap1p in oxidative stress response.