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Mitogen-activated protein kinase (MAPK) cascade is involved in the regulation of a series of biological processes in organisms, which are composed of <i>MAPKKKs</i>, <i>MAPKKs</i>, and <i>MAPKs</i>. Although genome-wide analyses of it has been well described in some species, little is known about <i>MAPK</i> and <i>MAPKK</i> genes in pomegranates. In this study, we identified <i>18 PgMAPKs</i>, <i>9 PgMAPKKs</i> through a genome-wide search. Chromosome localization showed that 27 genes are distributed on 7 chromosomes with different densities. Multiple sequence alignment and phylogenetic analysis revealed that <i>PgMAPKs</i> and <i>PgMAPKKs</i> could be divided into 4 subfamilies (groups A, B, C, and D), respectively. In addition, exon-introns structural analysis of each candidate gene has indicated high levels of conservation within and between phylogenetic groups. Cis-acting element analysis predicted that <i>PgMAPKs</i> and <i>PgMAPKKs</i> were widely involved in the growth, development, stress and hormone response of pomegranate. Expression profile analyses of <i>PgMAPKs</i> and <i>PgMAPKKs</i> were performed in different tissues (root, leaf, flower and fruit), and <i>PgMAPK13</i> was significantly expressed in all tissues. To our knowledge, this is the first genome-wide analysis of the <i>MAPK</i> and <i>MAPKK</i> gene family in pomegranate. This study provides valuable information for understanding the classification and functions of pomegranate MAPK signal.