The present study aimed to survey the prevalence of methicillin-resistant Staphylococcus aureus and Candida species oral and nasal co-colonization among patients with malignancies on chemotherapy in Tehran, Iran. In a cross-sectional single-center study performed from October until the end of December 2020, oral and nasal specimens were collected using dry sponge swabs from patients with different malignancies under chemotherapy in Masih Daneshvari Hospital, Tehran, Iran. We used the disk diffusion method to the screening of oxacillin (methicillin) resistance among S. aureus isolates. The final identification of MRSA strains and the frequency of hyphal adhesin Als3p was performed using the PCR method with a specific primer that targeted mecA and Als3p genes, respectively. A total of 170 oral and nasal specimens were collected from 170 adult patients. Oral colonization by S. aureus, MRSA, and Candida species was found in 20 (11.8%), 11 (6.5%), and 68 (40%) patients, respectively, while nasal colonization by S. aureus and MRSA and Candida species was found in 26 (15.3%), 17 (10%) and 7 (4.1%) patients, respectively. The total colonization of MRSA and Candida spp. in both oral and nasal was 14.7% (n = 25/170) and 41.2% (n = 70/170), respectively. All MRSA isolates and Candida species were positive for mecA and Als3p genes, respectively. The present study revealed the importance of polymicrobial infection among patients with different malignancies and presumed that S. aureus can use Candida adhesion Als3p to create systemic infections in immunocompromised patients.