Genome wide analysis of the genes responsible for polyphenol oxidase (PPO) or peroxidase (POX) enzymes was performed in nine plant species namely (Carica papaya), model plant dicot (Selaginella moellendorffi), monocot (Zea mays), legumes (pisum sativum, Vigna angularis), cereals (Avena sativa, Setaria italic and Oryza sativa) and fruit (Morus notabilis) species. We identified 135 PPO and 1645 POX genes in the selected plant species during the genome wide distribution analysis. . The result showed that A.sativa and P. sativum had no PPO genes and a few number of POX genes were found in these plants. The synteny analysis of PPO genes in seven plant species excluding A.sativa and P.sativum revealed higher degree of conservation, recommending that these genes occurred before monocot/ eudicot divergence. The gene ontology (GO) analysis showed that PPO gene (Accession no DQ532396.1; 577 amino acids) is localized maximum in chroplast (43.1%) with score of 2.156, molecular function (47.4%), biological process (53.7%) and cellular component (13.9%). While the POX protein (Accession no DQ855429.1; 335 amino acids) is highly founded in the extracellular part of the cell membrane (62.2%) with score 3.108, molecular function 49.8%, biological process 50.9% and cellular component 61.3%. Among the identified PPO and POX genes were reported to be (91.15%) and (85.21) moderately or highly expressed. The network analysis showed that PPO and POX genes had 21, 21 nodes, 100, 97 edges, 9.52, 9.24 average nodes and 0.876, 0.539 average local cluster coefficient respectively. The POX genes were located in sub-telomeric section of chromosomes in the form of clusters. This study about genome-wide investigation and consideration of gene-expression patterns generated the valuable evidence on PPO and POX gene families that will be helpful for improving crop production in monocot or dicot plants