Aim. S. aureus and S. epidermidis remain the leading biofilm-forming agents causing orthopedic implant-associated infections (OIAI), but other coagulase-negative Staphylococcus (CoNS) with clinical importance is emerging. Besides, few studies have assessed specific genomic traits associated with patient outcome. This is a preliminary descriptive study of phenotypic and genomic features identified in clinical isolates of S. aureus and CoNS isolates recovered from OIAIs patients that progressed to treatment failure. Methods. Ten isolates were identified by matrix-time-of-flight laser-assisted desorption mass spectrometry (MALDI-TOF-MS) and tested for antibiotic susceptibility and biofilm formation. Genotypic characteristics, including, MLST (Multi Locus Sequence Typing), SCCmec typing, virulence and resistance genes were assessed by whole-genome sequencing (WGS) that was performed on an Illumina HiSeq 2500 platform. Bioinformatics analyzes were performed using CGE, PATRIC, VFDB, CARD RGI, SnapGene, BLAST, and PubMLST. S. aureus (215, 260 and 371) isolates belonged to CC5 (ST5 and ST105, spa type t002) and carried SCCmec type I (1B), II (2A) and V(5C2), respectively. Results. They carried multiple resistance genes, with all resistant to methicillin (MRSA), and harboured mecA, blaZ. S. aureus 215 and 371 carried ermA gene and multiple genes for aminoglycosides resistance including aph(3’)-III, ant(9)-Ia, and ant(4)-Ib, and for quinolones. S. aureus 260 also carried resistance genes for tetracycline, quinolones and trimethoprim (dfrC). All MRSA were strong biofilm producers harboring the complete icaADBC and icaR operon, and also carried multiple adhesion and toxin-related virulence genes. Seven CoNS isolates comprising five species (S. epidermidis, S. haemolyticus, S. sciuri, S. capitis and S. lugdunensis) were analyzed, with mecA gene detection in five isolates. S. haemolitycus (95) and S. lugdunensis were unable to form biofilm and did not harbor the complete icaADBCR operon. S. epidermidis (216, 403) and S. haemolyticus (53,95) isolates belonged to the ST2/CC2, ST183, ST9 and ST3, respectively. High variability of adhesion genes was detected, with atl, ebp, icaADBC operon and IS256 being the most common. Conclusions. In conclusion, this study provides insights into the phenotypic and genomic analysis of Staphylococci allowing elucidation of MRSA and CoNS specific features that are associated with treatment failure in OIAIs, including genes associated with biofilm production, and resistance to β-lactam and aminoglycosides