MADS-box genes encode a family of transcription factors that participate in many developmental processes in plants. Among the ripening-related MADS-box genes isolated from banana, only MaMADS2 gene encodes a transcription factor involved in developmental regulation of fruit ripening. In this study, four complementary deoxyribonucleic acid (cDNA) isoforms of MADS2 gene were isolated from Musa acuminata Colla cv. Lakatan, named MalMADS2.1, MalMADS2.2a, MalMADS2.2b, and MalMADS2.3, and two isoforms from M. balbisiana Colla cv. Saba, named MbsMADS2.1 and MbsMADS2.2. All six MADS2 isoforms shared 90-100% homology with the original MaMADS2 sequence from M. acuminata Colla cv. Grand Nain. While the isoforms MalMADS2.2a and 2.2b have identical open reading frames and derived amino acid sequences, their 3′ untranslated regions (UTR) differed by showing insertion/deletion sites and different response elements. The putative elements identified were related to the expression of the stress response compounds such as methyl jasmonate and abscisic acid. Promoters for the dominant MADS2 isoforms were also isolated and sequenced. The cis-elements that were common to both cultivars were the light responsive elements (GATA motif, MNF1, and As-2-box) and the TCA element that is involved in the production of salicylic acid.