Background: Diversity of clones is common in Staphylococci, but the focus on this diversity is less in coagulase negative group. Objective: We aimed to detect the biodiversity of Staphylococcus epidermidis isolated from skin lesions. Methodology: S. epidermidis were identified using Gram stain, catalase and coagulase tests, cultured on mannitol salt agar and tested for antibiotic susceptibility. Biodiversity was assessed using PCR of 16s rRNA genes. Phylogenetic analysis of isolate's sequences and sequences of S. epidermidis retrieved from Gene bank was done. The sequences were aligned to show their degree of similarity. Results: About 86% and 57% were resistant to penicillin and cefoxitin, fusidic acid, and erythromycin; respectively. Phylogenetic analysis revealed all S. epidermidis involved were belonged to the same cluster with S. epidermidis strain AFATF that was isolated previously from Egypt Conclusion: We confirmed the usefulness of 16s rRNA gene sequence in phylogenetic studies and the biodiversity of our isolates.