MADS-box transcription regulators play important roles in plant growth and development. However, very few MADS-box genes have been isolated in the genusTaraxacum, which consists of more than 3000 species. To explore their functions in the promising natural rubber (NR)-producing plantTaraxacum kok-saghyz(TKS), MADS-box genes were identified in the genome of TKS and the related speciesTaraxacum mongolicum(TM; non-NR-producing) via genome-wide screening. In total, 66TkMADSsand 59TmMADSswere identified in the TKS and TM genomes, respectively. From diploid TKS to triploid TM, the total number of MADS-box genes did not increase, but expansion occurred in specific subfamilies. Between the two genomes, a total of 11 duplications, which promoted the expansion of MADS-box genes, were identified in the two species.TkMADSandTmMADSwere highly conserved, and showed good collinearity. Furthermore, mostTkMADSgenes exhibiting tissue-specific expression patterns, especially genes associated with the ABCDE model, were preferentially expressed in the flowers, suggesting their conserved and dominant functions in flower development in TKS. Moreover, by comparing the transcriptomes of different TKS lines, we identified 25TkMADSsrelated to biomass formation and 4TkMADSsrelated to NR content, which represented new targets for improving the NR yield of TKS.