Pemphigus is a chronic autoimmune blistering disease. Pemphigus blisters can damage the natural skin barrier and increase the risk of life-threatening conditions. Colonization of pemphigus wounds with methicillin-resistant Staphylococcus aureus (MRSA) prolongs wound healing and increases mortality rate. Assessing MRSA prevalence, types, and toxin and adhesion genes can facilitate the detection of MRSA strains which cause infections, selection of appropriate treatments, and healing of pemphigus wounds. This study aimed to determine the SCC mec , the direct repeat unit (dru) types (dts), and the toxin, MSCRAMM, and biofilm genes of MRSA strains isolated from pemphigus wounds. In this cross-sectional study, 118 S. aureus isolates were gathered from 118 patients with pemphigus. MRSA detection was performed using the mecA gene. Using the polymerase chain reaction method, all MRSA isolates were assessed for the presence of the sea , seb , sec , tst , eta , pvl , hla , hlb , MSCRAMM, and ica genes. Typing and subtyping were performed through respectively SCC mec typing and dru typing methods. The Bionumerics software was used for analyzing the data and drawing the minimum spanning tree. From 118 S. aureus isolates, 51 were MRSA. SCC mec typing revealed the prevalence of SCC mec II with a prevalence of 64.7% (33 out of 51 isolates) and SCC mec III with a prevalence of 35.3% (18 out of 51 isolates). Dru typing indicated seven dts, namely dts 10a, 10g, 10m, 13i, 8h, 8i, and 9ca in two main clusters. The dt9ca was a new dru type and was registered in the dru -typing database (www. dru -typing.org). The prevalence rates of the hla , sea , and sec genes in MRSA isolates were respectively 54.9%, 27.4%, and 1.9%, while the hlb , seb , eta , and pvl genes were not detected at all. Only one MRSA with SCC mec III and dt10a carried the tst encoding gene. MSCRAMM gene analysis revealed the high prevalence of the eno (31.3%) and the fib (21.5%) genes. The prevalence rates of the icaA and icaD biofilm formation genes were 3.9% and 5.8%, respectively. There were no significant differences between the two detected SCC mec types and between the two detected dts clusters respecting the prevalence of the encoding genes of virulence factors and MSCRAMMs. The toxin genes hla and sea are prevalent among MRSA strains with SCC mec II and III isolated from pemphigus wounds. The most prevalent dts are dt10a and dt10g among MRSA with SCC mec III and dt8h and dt8i among MRSA with SCC mec II. • A total of 118 Staphylococcus aureus isolates from Pemphigus wound infection were analyzed. • 51 isolates were identified as MRSA with SCC mec types II and III. • Dru typing indicated seven dts, namely dts 10a, 10 g, 10 m, 13i, 8 h, 8i, and 9ca in two main clusters. • The dt9ca was a new dru type and was registered in the dru -typing database • The prevalence rates of the hla and sea genes in MRSA isolates were 54.9% and 27.4% respectively. • MSCRAMM gene analysis revealed the high prevalence of the eno and the fib genes. [ABSTRACT FROM AUTHOR]