Objective To investigate the carrying status of methicillin-resistant Staphylococcus aureus (MRSA) resistance genes and virulence factor pvl gene in sputum of patients with healthcare-associated pneumonia(HAP). Methods Forty-six strains of MRSA from sputum of patients with HAP in an intensive care unit (ICU) of a hospital were detected resistance genes (mecA, aacA-D, tetK, tetM, msrA, msrB, ermA, ermC, vatA, vatB, vatC, femB and linA) and virulence factor pvl gene by polymerase chain reaction (PCR), SCCmec genotypes of MRSA strains were analyzed by PCR. Results Among 46 MRSA strains, detection rates of resistance genes mecA, aacA-D, tetK, msrA, ermA, ermC, femB, and linA were 100%, 54.35%, 36.96%, 13.04%, 36.96%, 52.17%, 71.74%, and 10.87% respectively. None of strains were detected tetM, msrB, vatA, vatB, and vatC genes; virulence factor pvl gene carrying rate was 65.22%. Four genotypes of SCCmec were detected among 46 MRSA strains, 26.09%, 52.17%, 2.17%, and 2.17% of which were SCCmec Ⅱ, Ⅲ, IVc, and V respectively. Conclusion MRSA carries multiple drug resistance genes in sputum of patients with HAP, virulence gene pvl is high, SCCmec genotype is mainly type Ⅲ, health care workers should pay highly attention.