The transcriptome of Anemone rivularis var. floreminore was sequenced by Illumina HiSeq 2000 platform to find flower development gene. The result indicated that 54 513 822 sequence reads containing 7 826 726 115 bp nucleotide sequence information were obtained. A total of 43 767 unigenes were formed by initial sequence splicing，with an average read length of 926 bp. Annotation analysis of unigene indicated that 28 130 unigenes had homolog in public protein database. Total 5 015 unigenes included SSRs and the highest frequency was AG/CT，followed by AAG/CTT and ACC/GGT. Through the analysis of transcription factors, 12 MIKCtype MADS genes closely related to flower development were selected，and they were FUL1，FUL2，AP31，AP32，AP33，PI1，PI2，AG1，AG2，SEP1，SEP3 and AGL6. Quantitative PCR analysis showed that the expression of FUL1，SEP1，SEP3 and AGL6 were significant up regulate in white，greenwhite，fiveflap and green plants than that in normal flower of A. rivularis var. floreminore，and the expression of 12 genes had no significant difference in normal and extreme variation plants. The expression of AGL6，SEP3，FUL1，PI2 and SEP1 were the main indexes of flower morphogenesis based on Principal Component Analysis (PCA). These results greatly enriched genetic information of A. rivularis var. floreminore and provided basic data for the study of mechanism on diversity of floral organ variants in A. rivularis var. floreminore in the future.