MADS-box genes encode a family of eukaryotic transcription factors distinguished by the presence of a highly-conserved ~58 amino acid DNA-binding and dimerization domain at the N-terminal (the MADS-box). In plants, MADS-box genes are best known as master regulators of flowering time and floral organ development, although they also function in the development of leaves, roots, fruit, seeds and gametophytes. Recent work in perennial species suggests an additional role for MADS-box genes in the control of seasonal dormancy. We identified 83 MADS box genes from the recently-sequenced genome of peach (Prunus persica), classified them into Types I (41 genes) and II (42 genes), and assigned a subset of the Type II genes to established subfamilies within the MIKCc clade. We determined exon-intron organization for all genes based on comparison with corresponding ESTs and homologous Arabidopsis genes. Phylogenetic analyses demonstrated significant expansion within the SVP subfamily relative to Arabidopsis, as well as a reduction within the FLC/MAF lineage. Analysis of the SVP subfamily across a number of perennial species indicated that expansion within this clade has occurred independently in multiple plant lineages. We used RNAseq data from apical buds, cotyledons, fruit, leaves and roots to determine tissue-specific expression levels of each MADS box gene. Although expression of Type I genes is typically limited to the female gametophyte in Arabidopsis, several peach Type I subfamilies showed significant expression in vegetative tissues. The majority of Type II genes were expressed in multiple tissues, including leaves and roots.