| Summary: | MIKC<sup>C</sup>-type MADS-box genes are involved in floral organ identity determination but remain less studied in the <i>Malus</i> lineage. Based on the conserved domains of this gene family, we identified 341 genes among 13 species. Classification results showed that the MIKC<sup>C</sup>-type were generated later than the M-type, after the formation of <i>Chlamydomonas reinhardtii</i>. By phylogenetic analysis, three different groups were divided among 12 plant species, and one group was an ancestral MIKC<sup>C</sup>-type MADS-box homologous gene cluster from lower moss to higher flowering plants. Comparative analysis of these genes in <i>A. thaliana</i> and <i>Malus</i> lineages revealed a similar pattern evolutionary relationship with the phylogenetic analysis. Three classes of genes of the ABC model in <i>A. thaliana</i> had orthologous genes in the <i>Malus</i> species, but they experienced different evolutionary events. Only a whole-genome duplication (WGD) event was considered to act on the expansion of ABC-model-related genes in the <i>Malus</i> lineage. Additionally, the expression pattern of genes showed to be involved in flowering development stages and anther development processes among different <i>M. domestica</i> cultivars. This study systematically traced the evolutionary history and expansion mechanism of the MIKC<sup>C</sup>-type MADS-box gene family in plants. The results also provided novel insights for ABC model research of flower development in the <i>Malus</i> lineage.
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