The expression of genes specific to floral organ is important for the floral organ formation and development in Medicago truncatula. Screening of the genes specifically expressed in M. truncatula flowers and comparing the expression patterns of their orthologous homologous genes among different model plants can provide novel insights into the functions of these genes in controlling the floral organ development in M. truncatula. According to the expression profile data of PISTILLATA (PI), we screened 97 genes specifically expressed in M. truncatula floral organs (ratio≥10 and Z≥7.9). Their homolog genes were also identified in Arabidopsis thaliana, soybean (Glycine max L.), Lotus japonicus, and rice (Oryza sativa L.). The results of comparing the gene expression levels, the gene expression patterns, and the gene functions among these species indicated that the expression variation of the orthologous homolog genes was small in the kindred species and was great in distant species. Furthermore, we compared the cis-acting regulatory elements of the genes, which had large expression variation among different plants. These results suggest that the great discrepancy of the orthologous homolog gene expression caused by the different character of cis-element in the promoter region.