A study was carried out to understand the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in selected seafood commodities, market environment as well as in aquaculture farms in Kerala, along the south-west coast of India. Two hundred and thirty three samples comprising finfish, crustaceans, molluscs and fishery environmental samples from markets as well as aquaculture farms were collected and screened for the presence of MRSA. The S. aureus isolates obtained from the samples were checked for resistance to methicillin, oxacillin and cefoxitin by antimicrobial sensitivity test and further confirmed by oxacillin agar screening method. A multiplex PCR was employed targeting mecA, nuc and 16s rDNA genes to differentiate S. aureus and MRSA from other staphylococci. It was found that 13.4% of the samples harboured MRSA while the overall prevalence of S. aureus was found to be 36.5%. This study has clearly indicated high prevalence of methicillin resistant S. aureus strains in the seafood as well as in environmental samples from seafood markets and aquaculture farms in Kerala. The prevalence of methicillin resistant strains of staphylococci in fish indicates high risk associated with fish handlers and fish farmers. Staphylococcus aureus, a well known pathogen of hospital acquired infection and food poisoning (Khan et al., 2015), is a commensal organism of skin and mucous membrane of different species of animals as well as human beings and is not generally considered as the normal microflora of fish (Huss, 1988; Mc Carthy et al., 2012). Remarkably, 20% of individuals are persistently and 30% are transiently colonised with S. aureus in the nose (Liu, 2009). When the methicillin sensitive S. aureus (MSSA) acquires the genes responsible for methicillin resistance, the organism causes higher morbidity and mortality in humans with prolonged period of hospitalisation and are called as methicillin resistant S. aureus (MRSA) (Datta and Huang, 2008). There are a few reports on the prevalence of S. aureus in fish and fishery products from local retail markets and imported samples (Ayulo et al., 1994;Simon and Sanjeev, 2007;Saito et al., 2011;Bujjamma and Padmavathi, 2015;Obaidat et al., 2015). MRSA and methicillin resistant coagulase negative staphylococci (MR-CoNS) are recognised as zoonotic multidrug resistant pathogens causing hospital and community acquired infections in humans as well as infections in animals (Dahms et al., 2014). Resistance to methicillin is determined by mecA, encoded for low affinity penicillin binding protein PBP2A (Beck et al., 1986). Non-mecA mediated methicillin resistance in S. aureus may be due to excess production of beta-lactamase resulting in low level resistance to oxacillin called as borderline oxacillin resistant Staphylococcus aureus (BORSA) (Maalej et al., 2012) or due to presence of a novel mecA gene homologue (mecALGA251 or mecC) causing resistance to beta-lactam antibiotics (Garcia-Alvarez et al., 2011). The prevalence of MRSA in fish was first reported from Malay...