Cytokinins (CKs) are a group of phytohormones that are involved in plant growth, development, and disease resistance. The isopentenyl transferase (IPT) and cytokinin oxidase/dehydrogenase (CKX) families comprise key enzymes controlling CK biosynthesis and degradation. However, an integrated analysis of these two gene families in radish has not yet been explored. In this study, 13 and 12 genes were identified and characterized, most of which had four copies in and two copies in radish and other diploid species. Promoter analysis indicated that the genes contained at least one phytohormone or defense and stress responsiveness cis-acting element. and were expanded through segmental duplication. Moreover, strong purifying selection drove the evolution of the two gene families. The expression of the and genes distinctly showed diversity in different tissues and developmental stages of the root. Expression profiling showed that was significantly upregulated in club-resistant materials during primary infection, suggesting their vital function in clubroot resistance. The interaction network of CKX proteins with similar 3D structures also reflected the important role of genes in disease resistance. This study provides a foundation for further functional study on the and genes for clubroot resistance improvement in .