Object Four regenerated somatic cell hybrids between carrot and Bupleurum scorzonerifolium Willd. proved by chromosome analysis were analyzed at the molecular level. Methods RAPD analysis and 5S rDNA spacer sequence were adopted. Results In the electrophoresis pattern of the PCR products the four somatic cell hybrids had the characteristic bands of two parents and new bands. Conclusion Their hybrid nature was clarified at molecular level. This provides a firm foundation to further analyze the main active components, saikosaponin of somatic cell hybrids, and screen out efficacious hybrid cell lines.