Allopolyploid plants have a wide distribution in the nature. The low-copy nuclear genes with special evolution characteristics and abundant phylogenetic information in polyploidy plant lineage show gene silencing, gene activation, and unequal expression in transcript level. In present review, focusing on the low-copy nuclear genes, we summarize the application of these genes in the phylogenetic reconstruction of allopolyploid plants and bring forward some critical issues in this field. In addition, we discuss the preliminary mechanisms of expression changes of these genes in polyploid plants, and introduce the progress and latest development in this field.