<p><i>Micrococcus luteus</i> strain ASd6, an endophytic bacterium isolated earlier from the medicinal plant <i>Andrographis paniculata</i> demonstrated significant enhancement in pharmaceutically important bioactive andrographolide content and plant growth. This study provides the first comprehensive whole genome analysis of <i>M. luteus</i> strain ASd6, aiming to uncover the genetic basis of its plant growth-promoting abilities. The genome of <i>M. luteus</i> ASd6 is of ~ 2.36 Mb with a GC content of 73%. The annotation identified 2,290 protein-coding genes were majorly found to be involved in plant beneficial traits such as phosphate solubilisation, nitrogen fixation, phytohormone production (indole-3-acetic acid (IAA), siderophores, and ACC deaminase biosynthesis). In addition to the unique genes, reactive oxygen species scavenging enzymes, heat shock proteins and cold shock proteins genes were also annotated which revealed their importance for better survival rate of the endophyte under adverse condition. Seed priming study showed colonization of <i>M. luteus</i> ASd6 with roots of <i>A. paniculata</i> seedlings. This genomic insight opens up exciting possibilities for future biotechnological applications in the area of plant microbe interaction with potential application of <i>M. luteus</i> ASd6 in sustainable agriculture.</p> Graphical Abstract <p></p>