AIMS: To investigate the distribution of staphylococcal enterotoxin genes (se) and the molecular features of community-associated methicillin-sensitive/resistant Staphylococcus aureus (CA-MSSA/MRSA) isolates in the nostrils of healthy pets and their owners. METHODS AND RESULTS: A total of 114 Staph. aureus isolates were identified from 1563 nasal swab samples, and CA-MRSA accounted for 20·2% (n = 23) of the total identified isolates. CA-MRSA isolates (91·3%, 21/23) harboured higher percentage of se than did CA-MSSA isolates (58·2%, 53/91) (P < 0·01), and the two highest se profiles of CA-MRSA were seb-sek-seq (42·9%, 9/21) and seb-sek-seq-sep (28·6%, 6/21). Of the MSSAs, 42·8% (39/91) were resistant to at least one antimicrobial drug and 8·8% (8/91) were multidrug resistant (MDR). We identified nine staphylocoagulase (SC) types (I-VIII and X) and three multilocus sequence types (ST59-MRSA-IV/V, ST-239-MRSA-V and ST241-MRSA-V). SC VII (23·4%, 22/94), a staphylococcal food poisoning isolate found mainly in Japan, and ST-59-MRSA-IV/V (85%, 17/20), a widespread CA-MRSA clone found mainly in Taiwan, both were the most predominant types. Phylogenetic analysis together with se and molecular characteristics obtained using pulsed-field gel electrophoresis showed that high levels of antimicrobial resistance and the se-carrying clone ST59-MRSA-IV/V-SC VII were all clustered in genogroup 5. CONCLUSIONS: The CA-MRSA clone of se-carrying-MDR-ST-59-IV/V-SC VII was identified predominantly in this study, and this clone might play a significant role in staphylococcal food poisoning in community settings. SIGNIFICANCE AND IMPACT OF THE STUDY: To our knowledge, this is the first study focussing on enterotoxin-carrying CA-MRSA/MSSA in pets and their owners, and the results support the future warnings in animal-human bond caused by CA-staphylococci in the commonwealth and the need to take cautions worldwide.