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Background  Cytokinin is a classical phytohormone that plays important roles in numerous plant growth and development processes. In plants, cytokinin signals are transduced by a two-component system, which involves many genes, including  cytokinin response factors  ( CRF s). Although  CRFs  take vital part in the growth of  Arabidopsis thaliana  and  Solanum lycopersicum , little information of the  CRFs  in the  Brassica  U-triangle species has been known yet.    Results  We identified and compared 141  CRFs  in the diploids and amphidiploids of  Brassica  species, including  B. rapa ,  B. oleracea ,  B. nigra ,  B. napus , and  B. juncea . For all the 141  CRFs , the sequence and structure analysis, physiological and biochemical characteristics analysis were performed. Meanwhile, the  Ka/Ks  ratios of orthologous and paralogous gene pairs were calculated, which indicated the natural selective pressure upon the overall length or a certain part of the  CRFs . The expression profiles of  CRFs  in different tissues and under various stresses were analyzed in  B. oleracea ,  B. nigra , and  B. napus . The similarities and differences in gene sequences and expression profiles among the homologous genes of these species were discussed. In addition,  AtCRF11  and its ortholog  BrCRF11a  were identified to be related to primary root growth in Arabidopsis.    Conclusion  This study performed a genome-wide comparative analysis of the  CRFs  in the diploids and amphidiploids of the  Brassica  U-triangle species. Many similarities and differences in gene sequences and expression profiles existed among the  CRF  homologous genes of these species. In the bioinformatics analysis, we found the close relativity of the  CRF  homologous genes in the  Brassica  A and C genomes and the distinctiveness of those in the B genome, and the  CRF  homologous genes in B subgenome were considerably influenced by the A subgenome of  B. juncea . In addition, we identified a new function of the Clade V  CRFs  related to root growth, which also clarified the functional conservation between  Arabidopsis  and  B. rapa . These results not only offer useful information on the functional analysis of  CRFs  but also provide new insights into the evolution of  Brassica  species.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5114-y) contains supplementary material, which is available to authorized users.

Comparative analysis of cytokinin response factors in Brassica diploids and amphidiploids and insights into the evolution of Brassica species