Daptomycin is a novel bactericidal agent active against Gram-positive pathogens including meticillin-resistant Staphylococcus aureus (MRSA). Our case is unique in the description of an MRSA USA 300 isolate that developed decreased susceptibility to daptomycin during daptomycin and vancomycin therapy. Directed sequencing detected a previously reported mutation in mprF, resulting in a T345A substitution, associated with non-susceptibility to daptomycin.