Stenotrophomonas MB339, a bacterium, which could potentially utilize aromatic compounds and tolerate different heavy metals was isolated from industrial wastewater. Subsequent experiments revealed strains ability to resist antibiotics ofloxacin, streptomycin, rifampicillin, erythromycin, ampicillin, clindamycin, and toxicants including As2+, Hg2+, Cu2+, Ni2+, Pb2+. The shotgun sequencing strategy, genome assembly and annotation uncovered specific features, which make this strain MB339 effectively promising to cope with highly contaminated conditions. This report presents isolate's assembled genome and its functional annotation identifying a set of protein coding genes (4711), tRNA (69 genes), and rRNA (9 genes). More than 2900 genes were assigned to various Clusters of Orthologous Groups (COGs) and 1114 genes attributed to 37 different Koyoto Encyclopedia of Genes and Genomes (KEGGs) pathways. Among these annotated genes, eighteen were for key enzymes taking part in xenobiotic degradation. Furthermore, 149 genes have been assigned to virulence, disease, and defense mechanisms responsible for multidrug and metal resistance including mercury, copper, and arsenic operons. These determinants comprised genes for membrane proteins, efflux pumps, and metal reductases, suggesting its potential applications in bioremediation.