Genetic diversity of 37 radishes (Raphanus sativus L.) with different fleshy colors collected from different areas of China was investigated using 86 SSR primers with distinct amplified bands. 86 SSR primers from 600 pairs of SSR primers in Brassica produced stable amplified bands and 976 bands were detected among the 37 accessions with 892 polymorphic bands, accounting for 91.39%. The mean number of alleles was 8.7 with a range from 2 to 20. The effective allelic number was 443.99 and accounted for 58.96%. Shannon’s index varied from 0.44 to 2.77 with an average of 1.76. On the basis of the genetic similarity coefficients, clustering analysis separated the 37 accessions into three groups. The cluster analysis showed that the accessions could be classified into three clusters when the genetic similarity was 0.81. Cluster I included six accessions of which are the white fleshy radishes, cluster II consisted of three red fleshy radishes and six white fleshy radishes, and cluster III composed by 22 accessions of which are the radishes with red fleshy. Genetic similarity coefficients of over 0.80 in the red and white fleshy radishes were 97 and 91%, respectively. The results above indicated that there was somewhat higher variation in the red than in the white fleshy radishes. The genetic similarity coefficient between the red and white fleshy radishes was 0.83 indicating genetically close relationship in radishes with different fleshy colors. In addition, it was deduced that the former may be a variant of the latter.