Fish provide important protein to human population. The procedures to preserve and maintain quality of fish from fishing until consumption can play a role in contamination with pathogens. Consumption of contaminated sea food products such as fish may lead to food poisoning. Knowledge about the spectrum of fish bacterial contaminants may assist in prevention of contamination and control food poisoning incidences. The present study aimed at characterizing and estimating prevalence of Staphylococcus aureus in fresh Indian Mackerel Fish (Rastrelliger kanagurta) from landing sites in Unguja Island. A total of 400 Indian Mackerel Fish were collected from landing sites in Unguja Island and from each fish two samples, skin swab and muscle, were collected. The primary culture was obtained from Mannitol salt agar, Nutrient and Blood agar followed by Gram staining, catalase coagulase tests. PCR targeting 16S rRNA, nuc, mecA, pvl, spa and enterotoxin genes was run to genetically characterize isolates and identify S. aureus. The result indicates that there was growth of bacteria in 359 (89.75%) fish skin swabs and 102 (25.5%) in fish muscle samples. Based on biochemical tests, 27 isolates (6.75%) were confirmed to be Staphylococcus bacteria. Of the 27 isolates, seven (1.75%) were confirmed S. aureus based on PCR. All 27 isolates confirmed to be positive in 16Sr RNA gene, two isolates demonstrated mecA gene and one had SEB and SEC. Detection of S. aureus in fresh Indian Mackerel Fish at landing sites poses a contamination risk to other critical points along the value chain and threatens public health