Methicillin-resistant Staphylococcus aureus (MRSA) is the most common cause of infectious diseases among athletes, globally. There is very little data on the prevalence of these strains in Kurdistan region of Iraq, and none on the carriage among athletes. This study aimed to determine the prevalence and associated risk factors with MRSA and molecular detection of mecA gene among athletes. This study was conducted in Zakho City, Kurdistan Region, Iraq, nasal swabs were collected from 510 participants among various types of athletes following the completion of a questionnaire. Traditional bacteriological methods were used for the isolation of MRSA Staphylococcus aureus and oxacillin susceptibility test was performed as a preliminary step in MRSA identification. Then MRSA isolates were further analysed by PCR in order to detect the mecA gene. Out of 510 participating athletes, MRSA nasal carriage rate was 8.04% (41/510). The highest rate of infection was observed among football (10.71%) followed by gym (9.39%), but there was no significant difference between the various types of sports with MRSA (p=0.41). There was a significant relationship between gender and type of athletes (p=0.018). Nasal colonization of MRSA was significantly influenced by body mass index (p=0.006), previous use of antibiotics (p=0.02), previous surgical operation (p=0.002), duration of training/ day (p=0.025) and number of training sessions/week (p=0.047). mecA gene was then confirmed in 38/40 (95%) MRSA isolates. The MRSA infection rate in our study was higher compared to other studies conducted elsewhere and was significantly higher among male athletes; this was associated with personal hygiene and inappropriate use of antibiotics. More studies were recommended on molecular analysis of virulent genes associated with MRSA in athletes.