Introduction: The laboratory of Training and Research in Medical Biology of Madagascar conducted a cross-sectional study to estimate the rate of S. aureus nasal carriage of pig and poultry Malagasy farmers. Methodology: Pig and poultry farmers from capital town of Madagascar were selected for nasal swabs collection with information on potential risk factors for S. aureus colonization, including animal exposure. Results: Nasal swabs from 180 farmers (M/F sex ratio: 0.74), enabled isolation after culture and biochemical identification, 69 (38.33%) S. aureus strains among which 45 (25%) were methicillin-resistant (MRSA). Risk factors analysis revealed that farming duration, number of animals, direct contact with poultry, and frequent contact with manure increased risk of S. aureus and MRSA nasal carriage. Likewise, farm practices that imply close contact with pigs such as food distribution and pigsty washing increased risk of S. aureus and MRSA nasal carriage among pig farmers. Among MRSA isolates, resistance rate to other antibiotics was similar to that of MRSA isolates from the non-farmer Malagasy population. However, gentamycin resistance was noticeably higher (32.5% versus 4.44%). Conclusions: This study shows a high rate of S. aureus and MRSA nasal carriage with high rate of multidrug resistance among healthy people frequently in contact with animals. A strategic policy against the spread of multidrug-resistant strains is desirable in farms and veterinary areas.