In this work, human serum albumin (HSA) stabilized gold nanoclusters (HSA-AuNCs) with reddish photoluminescence were used as sensing probes for pathogenic bacteria including Enterobacter cloacae, Escherichia coli J96, Pseudomonas aeruginosa, pandrug-resistant Acinetobacter baumannii (PDRAB), Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), Streptococcus pyogenes, and vancomycin-resistant Enterococcus faecalis (VRE). We discovered that HSA-AuNCs have unique affinity with S. aureus and MRSA. In addition to demonstrating the selective sensing ability of HSA-AuNCs toward S. aureus and MRSA, the binding peptide motifs identified from HSA-AuNCs were characterized by mass spectrometry. The identified binding peptides were further used as the reducing and stabilizing agents for generation of peptide-bound AuNCs (Pep-AuNCs). The generated Pep-AuNCs were demonstrated to have the binding affinities with S. aureus and MRSA.