Pseudomonas sp. P11 was isolated from the industrial wastewater sediment nearby the Daye Non-ferrous Metals Company, China. This strain possesses the ability to resist various heavy metals and efficiently precipitate arsenic. We here present a summary classification and a set of features of Pseudomonas sp. P11, together with the description of the genomic sequencing and annotation. The genomic sequence is 6,644,817 bp with a G+C content of 62.20% and contains 6143 protein-coding genes, 250 pseudo genes, and 76 tRNAs/rRNAs genes. Operons and gene clusters responsible for multiple heavy metal tolerance or detoxification were identified and accounted for the observed resistance phenotypes. Phylogenetic analysis revealed that the paralogous arsenic resistant genes possess different evolutionary paths. This study provides important insights to illuminate the versatility and adaptation of this strain to the heavy metal-contaminated environment.