Food handlers who carry enterotoxin-producing Staphylococcus aureus could become potential reservoirs of Staphylococcal food poisoning. The study is a cross-sectional one aimed to determine the prevalence of methicillin-resistant S. aureus (MRSA) and staphylococcal enterotoxins from randomly selected food handlers in Al Jazirah state, Sudan. Culture swabs were collected from the hands and nasals of food handlers (2016-2018). Identification of S. aureus was done on the basis of conventional laboratory tests. All S. aureus isolates were screened for MRSA and staphylococcal enterotoxin (SE) genes by polymerase chain reaction. The S. aureus strains were isolated from 25% of the collected culture swabs of which 42% were confirmed as MRSA. The existence of one or more of enterotoxin genes was confirmed in 34.4% of the isolated S. aureus strains. The combined staphylococcal enterotoxin genes were found in 9.6% of the isolates. The SE genes among MRSA strains (61.5%) were found to be higher than methicillin-sensitive S. aureus strains (14.8%). The most frequent staphylococcal enterotoxin genes were SEA (19.4%) followed by the SEB (8.6%), SEC (4.3%), and SED (2.1%). The carriage rate of MRSA strains demonstrated a higher rate of staphylococcal enterotoxins genes than methicillin-sensitive S. aureus. There is an increasing prevalence of MRSA compared with the previous rates and staphylococcal enterotoxin genes among Sudanese food handlers, which is a serious problem for public health.