<p>The ABCDE model is a well-known general model of floral development in angiosperms with perfect flowers, with some modifications in different plant taxa. The Fading Borders Model was proposed to better explain floral patterning in basal angiosperms that typically possess spirally arranged floral organs. The MADS-Box gene family is central to these models and has greatly expanded in higher plants which is associated with increasing complexity in floral structures. <i>Amborella trichopoda</i> is a basal angiosperm with simpler floral features, and the genetic and functional roles of MADS-Box genes in floral development remain poorly understood in the species. The major objectives of this study were to perform a genome-wide identification and characterization of MADS-Box genes in <i>A. trichopoda</i>, and to analyze their expression in floral buds and mature flowers. We identified 42 members of the MADS-Box gene family in <i>A. trichopoda</i> with a Hidden Markov Model (HMM)-based genome-wide survey. Among them, 27 were classified into Type II or MIKC group. Based on our classification and orthology analysis, a direct ortholog <i>APETALA1</i> (<i>AP1</i>), an A-class floral MADS-Box gene was absent in <i>A. trichopoda</i>. Gene expression analysis indicated that MIKC-type genes were differentially expressed between male and female flowers with B-function orthologs: <i>APETALA3</i> (<i>AP3</i>) and <i>PISTILLATA</i> (<i>PI</i>) in the species having differential expression between the two sexes, and E-function orthologs being upregulated in female flowers. Based on these findings, we propose a modification in the Fading Borders Model in <i>A. trichopoda</i> with a modified A-function, B- and E-function orthologs’ expression being sex-specific, and C- and D-function genes having roles similar to that in the classical ABCDE model. These results provide new insights into the genetics underlying floral patterning in the basal angiosperm.</p>