The study takes normal plant and tepal natural variant which have big differences in appearance as materials from wild Anemone rivularis var.flore-minore.The class B genes were isolated from genomes of normal plant and natural variant by using conventional and Hi-Tail PCR techniques.They were proved to be AP3-3 branch of paralogs which belong to AP3 gene family from B class MADS-box genes by sequence analysis and named NArAP3-3 (in normal plant) and VArAP3-3 (in natural variant),respectively.The full length of NArAP3-3 gene was 3 795 bp whereas 3 898 bp in VArAP3-3,they both have a 666 bp open reading frame (ORF) and can encode 221 amino acids.The protein showed a typical MADS-box gene structure containing MADS domain,K domain,Ⅰ region and C terminus.The comparison result of full length sequences between NArAP3-3 and VArAP3-3 genes was found to have a 49 bp insertion in VArAP3-3 gene,and there are also 4 base mutations in ORF sequence compared with the NArAP3-3 gene.By bioinformatics analysis of the two’s full length sequences,221 amino acids and insertion sequence,we can find that there are differences in all aspects of gene promoter,basic properties of protein,structure function domain,advanced prediction structure and so on.These differences may be one of the causes of tepals variation,and this study lays the foundation for the further exploration of its variation mechanism.