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Methicillin-resistant Staphylococcus lugdunensis (MRSL) is increasingly recognized in healthcare and community settings. To obtain a better understanding of the emergence of MRSL, this study characterized the structure and content of the SCC mec elements harboured by 36 MRSL isolates obtained from diverse sources in Hong Kong from 2008 to 2017. The isolates were investigated by whole-genome sequencing. SCC mec types and subtypes were assigned according to the guidelines from the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements. The sequence type (ST)-SCC mec combinations in the 36 MRSL isolates were as follows: ST3-SCC mec IV ( n =2), ST3-SCC mec V ( n =28), ST27-SCC mec V ( n =5) and ST42-SCC mec V ( n =1). The two SCC mec IV elements were highly similar to the SCC mec IV element harboured by the community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strain, JCSC6668. The J3 -mec complex-J2 regions in the SCC mec V elements were highly similar to the corresponding regions in the CA-MRSA strains PM1 ( n =13) or WIS ( n =21). Based on the J1 to J3 sequences, the SCC mec V elements can be categorized into nine different subtypes. Our findings highlight the diversified structures of SCC mec elements among MRSL strains and their close relationship with SCC mec elements harboured by CA-MRSA.