Here, we report complete genome sequences of two clinical isolates of
Staphylococcus aureus
, namely, Xen31 and Xen36, which have been genetically modified to express an optimized
Photorhabdus luminescens
luciferase operon. Xen31 and Xen36 are bioluminescent strains used widely for investigation of bacterial pathogenesis, drug discovery, and development of novel therapies.